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).

35 rows where measurement_class = "intrinsic" and sequence_status = "pending_manual_figure" sorted by kd_log10_molar

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Suggested facets: target_name_canonical, target_uniprot, aptamer_name, source_origin, pi_provenance_flag, assay_temperature_k, assay_buffer, aptamer_chemistry, aptamer_modifications, source_pmid, doi, source_db

assay_method 4

verification_level 2

target_type 2

tier 1

sequence_status 1

  • pending_manual_figure · 35 ✖

measurement_class 1

  • intrinsic · 35 ✖

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
143 P-selectin protein Q14242 PF377   14.0 pM -10.854 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF377 | 14 step2c_literal_v3
147 P-selectin protein Q14242 PF377sl   14.0 pM -10.854 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 296.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF377sl | 14 step2c_literal_v3
142 P-selectin protein Q14242 PF377   16.0 pM -10.796 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF377 | 16 step2c_literal_v3
144 P-selectin protein Q14242 PF377   18.0 pM -10.745 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 277.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF377 | 18 step2c_literal_v3
146 P-selectin protein Q14242 PF377sl   29.0 pM -10.538 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF377sl | 29 step2c_literal_v3
145 P-selectin protein Q14242 PF377sl   46.0 pM -10.337 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF377sl | 46 step2c_literal_v3
148 P-selectin protein Q14242 PF373sl   56.0 pM -10.252 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF373sl | 56 step2c_literal_v3
152 PDGF-BB protein P01127 PDGF-B aptamer   0.1 nM -10.0 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding         DNA 2'-fluoro; 2'-O-methyl; hexaethylene glycol spacer; inverted 3'-3' thymidine cap; 40-kd PEG conjugated 9916931 10.1016/S0002-9440(10)65263-7 the binding affinity of the aptamer used in the experiments described below ( K d ≈ 0.1 nM) step2c_literal_v3
149 P-selectin protein Q14242 PF398sl   178.0 pM -9.75 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF398sl | 178 step2c_literal_v3
50 PDGF-BB protein P01127 PDGF-specific aptamer   5e-10 M -9.301 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     microcantilever 310.15 7.4 PBSM buffer (10.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, and 1 mM MgCl2, pH 7.4) 1.0 DNA 3'-3'-linked thymidine nucleotide ([3'T]); thiolated 5'-end 24723743 10.1016/j.snb.2012.02.045 K d , as shown in Fig. 10, decreased from approximately 12 × 10 -10 M to 5 × 10 -10 M as the temperature changed from 19 to 37 ◦ C. step2c_literal_v3
4 sLe X -BSA glycan/conjugate Q9NSU2 Clone 2   8e-10 M -9.097 intrinsic Kd Gold v4 extraction_verified pending_manual_figure   KEEP_seq_in_figure SPR   7.4 RNA binding buffer [150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2] 1.0 RNA   11178986 10.1006/bbrc.2001.4327 Clone 2 | 9.8 3 10 5 | 7.3 3 10 2 5 | 1.2 3 10 9 | 8.0 3 10 2 10 step2c_literal_v3
150 P-selectin protein Q14242 PF422sl   1000.0 pM -9.0 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 PF422sl | 1 X 103 step2c_literal_v3
49 PDGF-BB protein P01127 PDGF-specific aptamer   1.2e-09 M -8.921 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     microcantilever 292.15 7.4 PBSM buffer (10.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, and 1 mM MgCl2, pH 7.4) 1.0 DNA 3'-3'-linked thymidine nucleotide ([3'T]); thiolated 5'-end 24723743 10.1016/j.snb.2012.02.045 K d , as shown in Fig. 10, decreased from approximately 12 × 10 -10 M to 5 × 10 -10 M as the temperature changed from 19 to 37 ◦ C. step2c_literal_v3
31 VWF A1-domain protein P04275 ARC1779   2.0 nM -8.699 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 298.15   Dulbecco's PBS containing 0.1 mg mL-1 BSA   DNA/RNA 2'-O-methyl; phosphorothioate; inverted deoxythymidine; 20-kDa PEG conjugation 19422452 10.1111/j.1538-7836.2009.03459.x This resulted in a final aptamer (ARC1779) that is a 40-nucleotide modified DNA/RNA oligonucleotide with a K D of 2 nM for the A1-domain. step2c_literal_v3
64 von Willebrand factor protein P04275 42-nt DNA aptamer   2.0 nM -8.699 intrinsic Kd Gold v4 extraction_verified pending_manual_figure   FLAG_cited_data ELISA     PBS with 1% BSA   DNA biotinylated 31493779 10.1055/s-0039-1696713 a biotinylated DNA aptamer was able to bind an antibody-captured VWF in a concentration-dependent manner with a dissociation constant ( KD ) of 2.0 nM 0.3. step2c_literal_v3
5 sLe X -BSA glycan/conjugate Q9NSU2 Clone 15   2.3e-09 M -8.638 intrinsic Kd Gold v4 extraction_verified pending_manual_figure   KEEP_seq_in_figure SPR   7.4 RNA binding buffer [150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2] 1.0 RNA   11178986 10.1006/bbrc.2001.4327 Clone 15 | 3.5 3 10 5 | 8.1 3 10 2 4 | 4.3 3 10 8 | 2.3 3 10 2 9 step2c_literal_v3
702 melatonin protein P48039 MLT-A-2   2.4 nM -8.62 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           text       36925277 10.1016/j.aca.2023.340971 K d = 2.4 ± 2.8 nM for MLT-A-2 elsevier_step2c
705 melatonin protein P48039 MLT-A-2F   2.4 nM -8.62 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           abstract       36925277 10.1016/j.aca.2023.340971 MLT-A-2F K d = 2.4 ± 2.8 nM elsevier_step2c
545 Human Cardiac Troponin I protein P19429 TnIApt 23   2.69 nM -8.57 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           abstract       26003883 10.1016/j.jbiotec.2015.05.002 Finally TnIApt 23 showed beast affinity in nanomolar range (2.69 nM) toward the target protein. elsevier_step2c
378 dT70 protein   DCC-SSB   3.0000000000000004e-09 M -8.523 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure                   34085169 10.1007/s12010-021-03585-x At a low concentration ( ∼ 2.5 nM), the titration with dT70 gave an approximate assessment of affinity ( K d ∼ 3 nM). step2c_acs_v1
6 sLe X -BSA glycan/conjugate Q9NSU2 Clone 18   3.9e-09 M -8.409 intrinsic Kd Gold v4 extraction_verified pending_manual_figure   KEEP_seq_in_figure SPR   7.4 RNA binding buffer [150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2] 1.0 RNA   11178986 10.1006/bbrc.2001.4327 Clone 18 | 5.1 3 10 5 | 2.0 3 10 2 3 | 2.5 3 10 8 | 3.9 3 10 2 9 step2c_literal_v3
7 sLe X -BSA glycan/conjugate Q9NSU2 Clone 4   7.4e-09 M -8.131 intrinsic Kd Gold v4 extraction_verified pending_manual_figure   KEEP_seq_in_figure SPR   7.4 RNA binding buffer [150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2] 1.0 RNA   11178986 10.1006/bbrc.2001.4327 Clone 4 | 4.1 3 10 5 | 3.1 3 10 2 3 | 1.3 3 10 8 | 7.4 3 10 2 9 step2c_literal_v3
569 MPT64 protein   aptamer sequence (17)   8.92 nM -8.05 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           text       28454652 10.1016/j.tube.2017.03.004 KD (dissociation equilibrium constant) was 8.92 nM elsevier_step2c
8 sLe X -BSA glycan/conjugate Q9NSU2 Clone 9   1e-08 M -8.0 intrinsic Kd Gold v4 extraction_verified pending_manual_figure   KEEP_seq_in_figure SPR   7.4 RNA binding buffer [150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2] 1.0 RNA   11178986 10.1006/bbrc.2001.4327 Clone 9 | 3.5 3 10 5 | 3.1 3 10 2 3 | 9.5 3 10 7 | 1.0 3 10 2 8 step2c_literal_v3
704 N-acetyl-5-hydroxytryptamine protein P46597 MLT-A-4F   0.016 μM -7.796 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           text       36925277 10.1016/j.aca.2023.340971 for NAT very low K d value was observed i.e., 0.016 μM elsevier_step2c
377 dT35 protein   DCC-SSB   2.9e-08 M -7.538 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure                   34085169 10.1007/s12010-021-03585-x The second stage was fitted to a hyperbola to give a K d value of 29 nM. step2c_acs_v1
346 Ciprofloxacin protein Q86VL8 R10K6   3.1e-08 M -7.509 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure                   30609709 10.3390/bios9010007 a dissociation constant (KD) for the RNA-ligand complex of 31 nM was determined. step2c_acs_v1
347 Ciprofloxacin protein Q86VL8 R10K6_V11   3.6000000000000005e-08 M -7.444 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure                   30609709 10.3390/bios9010007 The determined dissociation constant of 36 nM for V11 is similar to the original full-length aptamer R10K6 (31 nM). step2c_acs_v1
370 ODAM protein A1E959 OD64   4.771e-08 M -7.321 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure     SPR         DNA   33455205 10.1021/acsbiomaterials.0c01203 the obtained OD64 and OD35 (aptamer cognate pair) presented high a ffi nity and excellent speci fi city, along with dissociation constants ( K d ) of 47.71 nM (OD64) step2c_acs_v1
371 ODAM protein A1E959 OD35   5.1360000000000005e-08 M -7.289 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure     SPR         DNA   33455205 10.1021/acsbiomaterials.0c01203 the obtained OD64 and OD35 (aptamer cognate pair) presented high a ffi nity and excellent speci fi city, along with dissociation constants ( K d ) of 47.71 nM (OD64) and 51.36 nM (OD35). step2c_acs_v1
379 dT20 protein   DCC-SSB   2.4000000000000003e-07 M -6.62 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure       293.15           34085169 10.1007/s12010-021-03585-x Titrations of dT 27 and dT20 at low concentrations of DCCSSB gave smaller fluorescence changes, and the data were fit to give single K d values of 43 and 240 nM, respectively step2c_acs_v1
703 5-Methoxytryptamine protein P48039 MLT-C-1F   0.274 μM -6.562 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           text       36925277 10.1016/j.aca.2023.340971 For L-TRP and 5-MT very low K d were observed i.e., 0.324 μM and 0.274 μM respectively elsevier_step2c
380 dT20 protein   DCC-SSB   3.96e-07 M -6.402 intrinsic Kd Gold v4 multi_agent_verified pending_manual_figure       293.15           34085169 10.1007/s12010-021-03585-x With dT20, the intercept suggests a dissociation rate constant of 49 s -1 , producing a value of 396 nM for the equilibrium dissociation constant step2c_acs_v1
563 Brevetoxin-2 protein   Bap5   4.83 uM -5.316 intrinsic Kd Gold elsevier extraction_verified pending_manual_figure           text       28058132 10.1155/2016/9241860 The Kd value for the binding between the Bap5 aptamer and BTX-2 was 4.83 uM elsevier_step2c
151 P-selectin protein Q14242 NX244   9000000.0 pM -5.046 intrinsic Kd Gold v4 extraction_verified pending_manual_figure     filter_binding 310.15 7.4 SHMCK buffer 1.0 2'F-RNA   9743465 10.1089/oli.1.1998.8.265 NX244 | 9 X 106 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';