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).

119 rows where measurement_class = "intrinsic", sequence_status = "pending_manual_supp" and verification_level = "extraction_verified" sorted by kd_log10_molar

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Suggested facets: target_uniprot, source_origin, assay_temperature_k, assay_ph, assay_buffer, assay_cations, aptamer_modifications, source_db

assay_method 5

verification_level 1

  • extraction_verified · 119 ✖

tier 1

target_type 1

sequence_status 1

  • pending_manual_supp · 119 ✖

measurement_class 1

  • intrinsic · 119 ✖

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
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
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
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
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
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
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
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
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
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
605 human α-Thrombin protein P00734 A3   8.0 nM -8.097 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 For BLI it was found that aptamer A3 (8 nM and 25.5 nM) is the best binder elsevier_step2c
92 Okadaic Acid protein O95232 OA-LC2-TF   8.735 nM -8.059 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     BLI   7.5 50 mM Tris, 150 mM NaCl, 2 mM MgCl2, and 0.02% Tween-20 (pH 7.5) 2.0 DNA terminal fixation with GC-rich sequences 36322695 10.1021/acs.analchem.2c02653 The terminal-fixed OA-LC2 (OA-LC2-TF) exhibited a K d of 8.735 ± 0.606 nM step2c_literal_v3
613 human α-Thrombin protein P00734 B1   9.2 nM -8.036 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 For SCORE (Anabel analysis) the best is B1 (9.2 nM) elsevier_step2c
557 25-HydroxyvitaminD3 protein A0A0C5B5G6 VDBA14   11.0 nM -7.959 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       27520502 10.1016/j.bios.2016.08.011 the dissociation constants (Kd) of the VDBA14 was estimated to be 11 nM based on a non-linear regression method. elsevier_step2c
572 CTLA-4 protein P16410 aptCTLA-4   11.84 nM -7.927 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       28918052 10.1016/j.omtn.2017.08.006 dissociation constant (Kd) being 11.84 nM elsevier_step2c
101 thrombin protein P00734 Uyne A - AUyne   12.16 nM -7.915 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     BLI     buffer used for the bead-based selection, which contains Tween-20   DNA 5-ethynyl-2′-deoxyuridine (Uyne); Biotin (5' end) 37531184 10.1021/acschembio.3c00183 U yne A - AUyne | 12.16 ± 0.02 step2c_literal_v3
711 sST2 protein P30874 sS9_P   13.0 nM -7.886 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       37992929 10.1016/j.ijbiomac.2023.128295 The best performing aptamer candidate sS9_P (80mer) has shown affinity in low nanomolar range (~5.6 nM in ALISA and ~13 nM in ITC) elsevier_step2c
631 Bisphenol A protein O75897 38-mer BPA aptamer   13.17 nM -7.88 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       32113141 10.1016/j.foodchem.2020.126459 The K d values of the 63-mer, 38-mer, 12-mer and 23-mer aptamers were determined by using MST experiments, which were 491.69 nM, 13.17 nM, 27.05 nM and 1190.61 nM elsevier_step2c
100 thrombin protein P00734 Uyne A - Uyne Uyne   13.96 nM -7.855 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     BLI     buffer used for the bead-based selection, which contains Tween-20   DNA 5-ethynyl-2′-deoxyuridine (Uyne); Biotin (5' end) 37531184 10.1021/acschembio.3c00183 U yne A - U yne U yne | 13.96 ± 0.03 step2c_literal_v3
641 hexahistidine peptide protein   AptHis-1   15.0 nM -7.824 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       32739349 10.1016/j.ab.2020.113893 the Kd was as low as 15 nM (Table S1) elsevier_step2c
642 hexahistidine peptide protein   AptHis-2   15.0 nM -7.824 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       32739349 10.1016/j.ab.2020.113893 the Kd was as low as 15 nM (Table S1) elsevier_step2c
643 hexahistidine peptide protein   AptHis-3   15.0 nM -7.824 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       32739349 10.1016/j.ab.2020.113893 the Kd was as low as 15 nM (Table S1) elsevier_step2c
95 Dinophysistoxin protein   DTX-SL1-TF   15.45 nM -7.811 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     BLI   7.5 50 mM Tris, 150 mM NaCl, 2 mM MgCl2, and 0.02% Tween-20 (pH 7.5) 2.0 DNA terminal fixation 36322695 10.1021/acs.analchem.2c02653 DTX-SL1-TF showed a K d of 15.45 ± 1.92 nM step2c_literal_v3
612 human α-Thrombin protein P00734 B1   15.7 nM -7.804 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for SPR A2, B1 and B3 lay in the upper range (17 nM, 15.7 nM, 17.6 nM) elsevier_step2c
604 human α-Thrombin protein P00734 A2   17.0 nM -7.77 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for SPR A2, B1 and B3 lay in the upper range (17 nM, 15.7 nM, 17.6 nM) elsevier_step2c
617 human α-Thrombin protein P00734 B3   17.6 nM -7.754 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for SPR A2, B1 and B3 lay in the upper range (17 nM, 15.7 nM, 17.6 nM) elsevier_step2c
551 GTX1/4 protein   GO18-T-d   17.7 nM -7.752 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           abstract       26802576 10.1016/j.bios.2016.01.032 we truncated GTX1/4 aptamer and obtained the aptamer core sequence with a higher K d of 17.7 nM. elsevier_step2c
94 Dinophysistoxin protein   DTX-SL1   21.75 nM -7.663 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     BLI   7.5 50 mM Tris, 150 mM NaCl, 2 mM MgCl2, and 0.02% Tween-20 (pH 7.5) 2.0 DNA   36322695 10.1021/acs.analchem.2c02653 DTX-SL1 showed the lowest K d at 21.75 ± 1.42 nM step2c_literal_v3
552 GTX1/4 protein   GO18-T-d   21.9 nM -7.66 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       26802576 10.1016/j.bios.2016.01.032 Therefore, we further removed inactive nucleotides from GO18-T-a and obtained the core aptamer sequence GO18-T-d with a K d of 21.9 nM elsevier_step2c
707 prometryn protein   P60-1   23.0 nM -7.638 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       37453395 10.1016/j.talanta.2023.124838 The Kd value of P60-1 aptamer for prometryn was approximately 23 nM elsevier_step2c
665 16mer peptide from collagen XI alpha 1 chain protein   D1   25.0 nM -7.602 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       34815029 10.1016/j.aca.2021.339206 The K d values were identical (about 25 nM) elsevier_step2c
666 16mer peptide from collagen XI alpha 1 chain protein   C1   25.0 nM -7.602 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       34815029 10.1016/j.aca.2021.339206 The K d values were identical (about 25 nM) elsevier_step2c
606 human α-Thrombin protein P00734 A3   25.5 nM -7.593 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 For BLI it was found that aptamer A3 (8 nM and 25.5 nM) is the best binder elsevier_step2c
539 Staphylococcal enterotoxin B protein P01911 A2   26.0 nM -7.585 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       25624325 10.1128/AAC.04414-14 A2 and A11 both bound with high affinity to SEB, with dissociation constants of 26 nM and 64 nM, respectively elsevier_step2c
602 human α-Thrombin protein P00734 A2   26.4 nM -7.578 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 for iRIf aptamer A2 is the best (26.4 nM) elsevier_step2c
632 Bisphenol A protein O75897 12-mer BPA aptamer   27.05 nM -7.568 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       32113141 10.1016/j.foodchem.2020.126459 The K d values of the 63-mer, 38-mer, 12-mer and 23-mer aptamers were determined by using MST experiments, which were 491.69 nM, 13.17 nM, 27.05 nM and 1190.61 nM elsevier_step2c
608 human α-Thrombin protein P00734 A3   34.6 nM -7.461 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 For SCORE (Anabel analysis) the best is B1 (9.2 nM) and the poorest A3 (34.6 nM) elsevier_step2c
720 Zearalenone protein Q6UWP2 M1   35.83 nM -7.446 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       38608399 10.1016/j.foodchem.2024.139127 resulting in a slightly higher Kd value of 35.83 nM elsevier_step2c
611 human α-Thrombin protein P00734 B1   37.0 nM -7.432 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       31129134 10.1016/j.ab.2019.05.012 and the poorest B1 (37 nM) elsevier_step2c
731 ceftiofur protein   Apt-9   37.68 nM -7.424 intrinsic Kd Gold elsevier extraction_verified pending_manual_supp           text       40203705 10.1016/j.bios.2025.117446 Kd values for the binding of Apt-9 to cefapirin, cefquizime, and ceftiofur were ... 37.68 nM elsevier_step2c
99 thrombin protein P00734 TA-AT   38.7 nM -7.412 intrinsic Kd Gold v4 extraction_verified pending_manual_supp     BLI     buffer used for the bead-based selection, which contains Tween-20   DNA Biotin (5' end) 37531184 10.1021/acschembio.3c00183 TA - AT | 38.7 ± 0.5 step2c_literal_v3

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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';