Binding affinities (Kd) — source-verified (view)

742 distinct verbatim-verified aptamer–target Kd measurements (canonical Gold v1; 555 intrinsic-equilibrium; 300 unique targets; 287 publications; 435 carry a verbatim-verified sequence). ★HOW TO READ: 'kd_reported' is the value EXACTLY as written in the paper (units are MIXED — pM/nM/M — so it is NOT directly comparable). To compare, sort, or train an ML model, use ONLY 'kd_log10_molar' (lower = tighter) and filter measurement_class=intrinsic + target_type=protein. The same target appears in several rows because of different aptamers, assays, conditions (temperature/buffer) or papers — see those columns. For a clean ready-to-use subset use the 'kd_ready_to_use' query. Source: corpus literature-extraction pipeline (E. Dohi).

Data license: CC BY 4.0 · Data source: apt-scout automated curation pipeline (E. Dohi, NCNP) — values harvested from public databases; raw source stored per target

target_name_canonical
Target as named in the source paper.
target_type
protein / cell-line+EV / glycan-conjugate. Filter to 'protein' for molecular targets.
target_uniprot
UniProt accession when a human protein (sparse for now; links to apt-scout target).
aptamer_name
Aptamer identifier as reported.
kd_reported
Kd value AS REPORTED in the paper (value + unit). Units are MIXED — do NOT compare this column directly.
kd_log10_molar
log10(Kd in molar). THE column to sort / compare / learn on (lower = tighter).
measurement_class
intrinsic = equilibrium vs purified target; non_intrinsic = apparent/cellular or avidity (NOT comparable to intrinsic).
binding_constant_type
Kd / apparent-Kd etc. as reported.
assay_method
SPR / filter binding / flow cytometry / ITC / BLI …
assay_temperature_k
Assay temperature (K) — a reason the same pair can have several rows.
source_pmid
PubMed ID of the source paper (links out).
verbatim_quote
The exact sentence the value was taken from.
verification_level
QC status (honest, growing): human_verified / human_corrected = a logged human verdict from the stratified-random sample; multi_agent_verified = passed independent multi-agent (L2) check; extraction_verified = extraction-pipeline verified; automated. Human verification is in progress: as of this release 0 records carry a logged human verdict — the published set is multi-agent-/extraction-verified, and human spot-checking is being added post-publication (version-tracked). No record is labelled human_verified without a logged human review.
sequence_status
Aptamer-sequence provenance: verified_in_text_or_SI = sequence verbatim-verified against the source text/SI (shown); pending_manual_supp / pending_supp_oa / pending_manual_figure = sequence reported only in a (often paywalled) SI or a figure, being curated post-submission; no_single_sequence_pool = a pool/library/primer, no single sequence exists.
pi_provenance_flag
PI manual-review flag: KEEP_seq_in_figure = valid record, sequence is in a 3D-structure figure; FLAG_cited_data = Kd may be a value cited from elsewhere, re-verify. (EXCLUDE rows are hidden from this view.)
seq_source
original (already in source DB) / backfill_text_verified (recovered from paper or SI text).

207 rows where sequence_status = "pending_manual_supp" sorted by kd_log10_molar

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Suggested facets: source_origin, assay_temperature_k, assay_ph, assay_cations, aptamer_chemistry, source_db

assay_method 13

verification_level 2

target_type 2

tier 1

sequence_status 1

  • pending_manual_supp · 207 ✖

binding_constant_type 1

id target_name_canonical target_type target_uniprot aptamer_name aptamer_seq kd_reported kd_log10_molar ▼ measurement_class binding_constant_type tier source_origin verification_level sequence_status seq_source pi_provenance_flag assay_method assay_temperature_k assay_ph assay_buffer assay_cations aptamer_chemistry aptamer_modifications source_pmid doi verbatim_quote source_db
188 PDGF-BB protein P01127 36aApt   0.036 pM -13.444 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 36aApt | 0.036 ± 0.012 | - 18.33 step2c_literal_v3
186 PDGF-BB protein P01127 38aApt   0.094 pM -13.027 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 38aApt | 0.094 ± 0.008 | - 17.76 step2c_literal_v3
598 human α-Thrombin protein P00734 A1   2.0 pM -11.699 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 Also for aptamer A1 we measured with MST KD values in the pico- and nanomolar range (2 pM and 52 nM). The lowest KD value is determined with MST (shown as bar) for aptamer A1, which is 2 pM. elsevier_step2c
406 SARS-CoV-2 spike protein (wild type) protein   DSA1N5   3e-12 M -11.523 avidity_multivalent Kd Gold v4 multi_agent_verified pending_manual_supp     dot_blot     undiluted wastewater   DNA dimeric 36926840 10.1021/acssensors.2c02655 DSA1N5 also demonstrated high binding affinity in undiluted wastewater samples ( K d = 3.0 -3.9 pM for WTPV, Figure S1A,B). step2c_acs_v1
208 SW480 cells cell/EV Q16520 Apt-nanovesicle   3.66 pM -11.437 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA cholesterol; multivalent 32049531 10.1021/jacs.9b13782 The dissociation constant ( K d ) value of Apt-nanovesicle against SW480 cells was found to be 3.66 ± 0.34 pM (Figure 2B) step2c_literal_v3
743 SARS-CoV-2 spike protein (wild type) protein   DSA1N5   3.9e-12 M -11.409 avidity_multivalent Kd Gold ACS multi_agent_verified pending_manual_supp     dot_blot     undiluted wastewater   DNA dimeric 36926840 10.1021/acssensors.2c02655 DSA1N5 also demonstrated high binding affinity in undiluted wastewater samples ( K d = 3.0 -3.9 pM for WTPV, Figure S1A,B). step2c_acs_v1
404 SARS-CoV-2 pseudotyped lentivirus (omicron variant) protein   DSA1N5   4.8e-12 M -11.319 avidity_multivalent Kd Gold v4 multi_agent_verified pending_manual_supp     dot_blot     deionized water   DNA dimeric 36926840 10.1021/acssensors.2c02655 This study demonstrates that DSA1N5 has high affinity for recognizing OMPV with a K d value of 4.8 pM, which is in the same order of magnitude as that measured for the WTPV (2.1 pM) in deionized water (DI water) step2c_acs_v1
405 SARS-CoV-2 pseudotyped lentivirus (omicron variant) protein   DSA1N5   5.1e-12 M -11.292 avidity_multivalent Kd Gold v4 multi_agent_verified pending_manual_supp     dot_blot     wastewater (diluted 50% with binding buffer)   DNA dimeric 36926840 10.1021/acssensors.2c02655 DSA1N5 preserves its binding affinity in 50% wastewater ( K d = 2.1 -4.1 pM for WTPV and 5.1 for OMPV in wastewater). step2c_acs_v1
184 PDGF-BB protein P01127 FullApt   5.33 pM -11.273 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 FullApt | 5.33 ± 2.36 | - 15.37 step2c_literal_v3
185 PDGF-BB protein P01127 40Apt   5.92 pM -11.228 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 40Apt | 5.92 ± 1.13 | - 15.31 step2c_literal_v3
187 PDGF-BB protein P01127 38bApt   7.03 pM -11.153 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 38bApt | 7.03 ± 1.28 | - 15.21 step2c_literal_v3
269 thrombin protein P00734 HD1-12A-DAB   13.1 pM -10.883 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     filter_binding     selection buffer   DNA   41053535 10.1002/advs.202509867 HD1-12A-DAB EXACT inhibitor bound to thrombin and prothrombin with K D s of 13.1 pm step2c_literal_v3
351 thrombin protein P00734 Supra-TBA15/29-GO   1.9e-11 M -10.721 avidity_multivalent Kd Gold v4 multi_agent_verified pending_manual_supp               DNA Graphene Oxide immobilization; poly(adenine) anchor 31157200 10.3389/fchem.2019.00280 Supra-TBA15 / 29-GO prepared with GO (40 μ g mL -1 ) at 60 ◦ C exhibited much higher binding affinity toward thrombin ( K d = 1.9 × 10 -11 M, Figure S10 , Supporting Information). step2c_acs_v1
209 SW480 cells cell/EV Q16520 Fixed Apt-nanovesicle   28.06 pM -10.552 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA cholesterol; crosslinked 32049531 10.1021/jacs.9b13782 the K d value of fi xed Apt-nanovesicles to SW480 cells was increased to 28.06 ± 3.31 pM (Figure 2D) step2c_literal_v3
56 von Willebrand factor A1-domain protein P04275 Rn-DsDsDs-53mh   61.3 pM -10.213 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR 310.15   1 × PBS supplemented with 0.05% (w/v) Nonidet P-40   DNA Ds (7-(2-thienyl)imidazo[4,5b]pyridine); mini-hairpin DNA 27966933 10.1021/jacs.6b10767 RnDsDsDs-53mh ( K D = 61.3 pM) step2c_literal_v3
542 Myoglobin protein P02144 anti-Mb aptamer   65.0 pM -10.187 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       25957831 10.1016/j.bios.2015.04.089 The corresponding af fi nity, K D, values calculated from the ratio between dissociation ( k d) and association ( k a ) was found to be 65 pM. elsevier_step2c
53 von Willebrand factor A1-domain protein P04275 Rn-DsDsDs-44   74.9 pM -10.126 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR 310.15   1 × PBS supplemented with 0.05% (w/v) Nonidet P-40   DNA Ds (7-(2-thienyl)imidazo[4,5b]pyridine) 27966933 10.1021/jacs.6b10767 Rn-DsDsDs-44 ( K D = 74.9 pM) exhibited the highest a ffi nity step2c_literal_v3
219 CCRF-CEM cells cell/EV Q9NRR3 CDN-sgc8   0.08 nM -10.097 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     fluorescence     1 × PBS, 5 mM MgCl2 5.0 DNA biotinylated 35670775 10.1021/acs.analchem.2c01359 Kd=0.08±0.01 nM step2c_literal_v3
57 von Willebrand factor A1-domain protein P04275 Rn-DsDs-51mh2   182.0 pM -9.74 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR 310.15   1 × PBS supplemented with 0.05% (w/v) Nonidet P-40   DNA Ds (7-(2-thienyl)imidazo[4,5b]pyridine); mini-hairpin DNA 27966933 10.1021/jacs.6b10767 Rn-DsDs-51mh2 ( K D = 182 pM) step2c_literal_v3
55 von Willebrand factor A1-domain protein P04275 ARC1172-41   326.0 pM -9.487 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR 310.15   1 × PBS supplemented with 0.05% (w/v) Nonidet P-40   DNA   27966933 10.1021/jacs.6b10767 ARC1172-41 ( K D = 326 pM) step2c_literal_v3
478 FLRPp (O serotype) protein   FMD_1   3.46e-10 M -9.461 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     SPR         DNA   42010751 10.1021/acs.analchem.5c04748 dissociation constants ( KD ) of 3.46 × 10 -10 M step2c_acs_v1
218 CCRF-CEM cells cell/EV Q9NRR3 mono-CDN-sgc8   0.48 nM -9.319 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     fluorescence     1 × PBS, 5 mM MgCl2 5.0 DNA biotinylated 35670775 10.1021/acs.analchem.2c01359 Kd= 0.48 ± 0.04 nM step2c_literal_v3
205 thrombin protein P00734 TBA29   0.5 nM -9.301 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA   31614078 10.1021/acs.analchem.9b03368 The 29-nt TBA29 aptamer has a bimodular duplex-antiparallel G4 structure and binds to thrombin with a binding a ffi nity of 0.5 nM. 30 step2c_literal_v3
550 Thrombin protein P00734 TBA29   5e-10 M -9.301 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       26643617 10.1016/j.jconrel.2015.11.028 and TBA29 (~5 × 10 -10 M) elsevier_step2c
303 EGFR protein P00533 Anti-EGF receptor aptamer   0.62 nM -9.208 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA 3' end sulfhydryl group (-SH) 41877526 10.1021/acs.molpharmaceut.5c01966 Anti-EGF receptor aptamers ( K d : 0.62 nM, DNA aptamers) step2c_literal_v3
536 tetracycline protein Q14728 TC aptamer   770.0 pM -9.114 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       25517161 10.1016/j.bpj.2014.11.001 dissociation constant Kd of 770 pM ([Mg 2 þ ] 1⁄4 10 mM) elsevier_step2c
459 PSMA protein Q04609 C3   8.000000000000001e-10 M -9.097 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     EMSA     5 mM Mg2+   DNA phenol-dT; naphthyl-dC; PSMA-617 bait 41126016 10.1021/jacs.5c13307 an exemplar shows very high affinity for PSMA ( K d ∼ 0.8 nM). step2c_acs_v1
217 CCRF-CEM cells cell/EV Q9NRR3 individual sgc8   0.82 nM -9.086 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     fluorescence     1 × PBS, 5 mM MgCl2 5.0 DNA biotinylated 35670775 10.1021/acs.analchem.2c01359 Kd=0.82 ± 0.12 nM step2c_literal_v3
458 PSMA protein Q04609 C3 (without fluorescein)   1e-09 M -9.0 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     EMSA         DNA phenol-dT; naphthyl-dC; Cy5 label 41126016 10.1021/jacs.5c13307 EMSA data show that Cy5-labeled C3 without fluorescein binds PSMA just as strongly as the parent construct, with an apparent K d of ∼ 1 nM (Figure S9). step2c_acs_v1
54 von Willebrand factor A1-domain protein P04275 Pr-DsDsDs-40   1.03 nM -8.987 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR 310.15   1 × PBS supplemented with 0.05% (w/v) Nonidet P-40   DNA Ds (7-(2-thienyl)imidazo[4,5b]pyridine) 27966933 10.1021/jacs.6b10767 Pr-DsDsDs-40 ( K D = 1.03 nM) step2c_literal_v3
664 PD-L1 protein Q9NZQ7 8-60   1.4 nM -8.854 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       34711320 10.1016/j.aca.2021.339066 8 e 60, a representative aptamer with high af fi nity (KD 1⁄4 1.4 nM determined by SPR) elsevier_step2c
108 thrombin protein P00734 T.7   1.5 nM -8.824 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR     binding buffer supplemented with 0.05% of Tween-20   DNA   37798416 10.1038/s41587-023-01973-8 T.7 exhibited the strongest binding signal with a 1.5 nM K d step2c_literal_v3
337 human α-thrombin protein P00734 LOOPER modified thrombin aptamer   1.6000000000000003e-09 M -8.796 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     SPR         DNA diversely functionalized; heteromultivalent 28938065 10.1021/jacs.7b07241 Using single-cycle kinetics surface plasmon resonance (SPR), the LOOPER aptamer exhibited a Kd of 1.6 nM step2c_acs_v1
228 CD8 protein P01732 A3t   2.0 nM -8.699 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA   36149728 10.1021/acsami.2c11783 A3t, a CD8 receptor-binding aptamer, which binds CD8-expressing cells with an equilibrium dissociation constant K D of 2 nM. step2c_literal_v3
232 CD8 protein P01732 rvCD8apt   2.0 nM -8.699 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA 8 nt toehold 36149728 10.1021/acsami.2c11783 apparent K D = 2 nM for CD8 + cells step2c_literal_v3
316 CD44-HABD protein   Motif 4 (ADDA adduct)   2e-09 M -8.699 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   23057694 10.1021/bi300471d motifs 2 and 4(ADDA adduct) have ~2 nM affinity to CD44-HABD step2c_acs_v1
322 S-adenosylmethionine protein P17707 Bs SAM-I riboswitch   3.0000000000000004e-09 M -8.523 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   23343213 10.1021/ja310742m Both μ MSA values agree well with results from the in-line probing assays performed using identical buffer conditions: ... 3 nM K d , respectively step2c_acs_v1
323 S-adenosylmethionine protein P17707 Pi SAM-I riboswitch   3.0000000000000004e-09 M -8.523 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   23343213 10.1021/ja310742m which is on the order of the 3 nM value measured using a conventional inline probing assay step2c_acs_v1
211 K562 protein Q8WUY8 PAM   3.2 nM -8.495 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA FAM 32307868 10.1002/anie.202004206 the K d value (3.2 nM) of PAM in binding the K562 cell is one order of magnitude lower than that of the aptamer alone (41 nM). step2c_literal_v3
614 human α-Thrombin protein P00734 B1   3.4 nM -8.469 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for MST the B aptamers (B1: 3.4 nM, B2: 5 nM, B3: 7.6 nM) elsevier_step2c
338 human α-thrombin protein P00734 LOOPER modified thrombin aptamer   4e-09 M -8.398 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   28938065 10.1021/jacs.7b07241 Preliminary binding analysis by label-free microscale thermophoresis showed a promising dissociation constant K d = 4 nM for thrombin step2c_acs_v1
465 SARS-CoV-2 spike RBD protein   Aptx2-L   4.900000000000001e-09 M -8.31 avidity_multivalent Kd Gold v4 multi_agent_verified pending_manual_supp     flow_cytometry 298.15 7.4 PBS, pH 7.4, 0.55 mM MgCl2   DNA   41498844 10.1021/acsami.5c16490 The Aptx2-L variant showed superior affinity with a dissociation constant ( K d) of 4.9 nM step2c_acs_v1
615 human α-Thrombin protein P00734 B2   5.0 nM -8.301 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for MST the B aptamers (B1: 3.4 nM, B2: 5 nM, B3: 7.6 nM) elsevier_step2c
710 sST2 protein P30874 sS9_P   5.6 nM -8.252 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       37992929 10.1016/j.ijbiomac.2023.128295 in case of sS9, parent aptamer has outperformed its truncated counterpart in terms of affinity as it has shown higher affinity (Kd ~5.6 nM). elsevier_step2c
603 human α-Thrombin protein P00734 A2   6.3 nM -8.201 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for SCORE (b-nd analysis) the best are A2 (6.3 nM) elsevier_step2c
461 Lipopolysaccharide from Klebsiella pneumoniae ATCC 15380 protein   aptamer seq. 5   6.68e-09 M -8.175 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     DPV     1 × PBS   DNA biotin 41323700 10.1039/d5ra06759f The binding affinity of aptamer seq. 5 was 6.68 nM (Fig. 9C). step2c_acs_v1
609 human α-Thrombin protein P00734 A3   6.9 nM -8.161 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for SCORE (b-nd analysis) the best are A2 (6.3 nM) and A3 (6.9 nM) elsevier_step2c
139 PTK7 protein Q13308 4AsF   7.2 nM -8.143 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     SPR 310.15 7.4 1 × DPBS 5.0 DNA SF at positions A23, A24, A25, A26 41065179 10.1021/jacs.5c11823 4AsF, which exhibited a 10-fold reduction compared to 4APS (0.77 vs 7.20 nM) step2c_literal_v3
556 VEGF165 protein P15692 cot-pega   7.33 nM -8.135 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       26956592 10.1016/j.jconrel.2016.03.006 The K D of cot-pega for VEGF was 7.33 nM (Fig. 1b) elsevier_step2c
616 human α-Thrombin protein P00734 B3   7.6 nM -8.119 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for MST the B aptamers (B1: 3.4 nM, B2: 5 nM, B3: 7.6 nM) elsevier_step2c

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CREATE VIEW v_kd AS
SELECT k.id,
 target_name_canonical,
 CASE
   WHEN target_name_canonical LIKE '%cell%' OR target_name_canonical LIKE '%vesicle%' OR target_name_canonical LIKE '%exosome%' THEN 'cell/EV'
   WHEN target_name_canonical LIKE '%BSA%' OR target_name_canonical LIKE '%sLe%' OR target_name_canonical LIKE '%glycan%' OR target_name_canonical LIKE '% Le %' THEN 'glycan/conjugate'
   ELSE 'protein'
 END AS target_type,
 target_uniprot, aptamer_name, aptamer_seq,
 (COALESCE(kd_value,'') || CASE WHEN COALESCE(kd_unit,'')!='' THEN ' '||kd_unit ELSE '' END) AS kd_reported,
 CAST(NULLIF(kd_log10_molar,'') AS REAL) AS kd_log10_molar,
 measurement_class, binding_constant_type, 'Gold' AS tier, k.tier AS source_origin,
 CASE
   WHEN vh.verdict='confirmed' THEN 'human_verified'
   WHEN vh.verdict='corrected' THEN 'human_corrected'
   WHEN vh.verdict='rejected'  THEN 'human_rejected'
   WHEN k.verification_status='agent_verified_L2' THEN 'multi_agent_verified'
   WHEN k.verification_status IN ('verified','CONFIRM') THEN 'extraction_verified'
   ELSE 'automated'
 END AS verification_level,
 sequence_status, seq_source, pi_provenance_flag,
 assay_method,
 CAST(NULLIF(assay_temperature_k,'') AS REAL) AS assay_temperature_k,
 CAST(NULLIF(assay_ph,'') AS REAL) AS assay_ph,
 assay_buffer, assay_cations, aptamer_chemistry, aptamer_modifications,
 source_pmid, doi, verbatim_quote, source_db
FROM kd_measurements k LEFT JOIN verification_human vh ON vh.row_id=k.source_record_id
WHERE LOWER(COALESCE(k.include_in_gold,''))='true';