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).

44 rows where measurement_class = "intrinsic", sequence_status = "pending_manual_supp" and verification_level = "multi_agent_verified" sorted by kd_log10_molar

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Suggested facets: target_name_canonical, target_uniprot, assay_temperature_k, assay_ph, assay_buffer, aptamer_chemistry, aptamer_modifications, source_pmid, doi

assay_method 6

verification_level 1

  • multi_agent_verified · 44 ✖

tier 1

target_type 1

sequence_status 1

  • pending_manual_supp · 44 ✖

measurement_class 1

  • intrinsic · 44 ✖

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
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
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
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
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
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
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
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
348 NP protein Q16612 NP-C04   8.1e-09 M -8.092 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   7.4 20 mM HEPES, 150 mM NaCl, 2 mM KCl, 2 mM MgCl2, and 2 mM CaCl2 (pH 7.4)   DNA FAM 30740973 10.1021/acs.analchem.8b04623 the K d values of NP-D01, NP-C04, and NP-D02 were 76..1 ± 10.9, 8.1 ± 2.4, and 41.3 ± 9.5 nM, respectively. step2c_acs_v1
423 TAR RNA protein Q13395 TAR RNA aptamer (best binding)   9.000000000000001e-09 M -8.046 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   39167715 10.1021/jacs.4c08824 A Biolayer Interferometry (BLI) experiment revealed that TAR RNA aptamers with the best binding affinity exhibited the dissociation constant ( K D) at 9 nM step2c_acs_v1
345 streptavidin protein   S8   1e-08 M -8.0 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   30520292 10.1021/acssensors.8b00945 At pH 7.4, we determined that S8 has a K d of 10 nM step2c_acs_v1
366 trastuzumab protein Q9ULR3 CH1S-3   1.0300000000000001e-08 M -7.987 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     MST 298.15   washing bu ff er with the addition of 0.005% Tween 20   DNA 5'-Cy5 32516525 10.1021/jacs.9b13370 a ffi nity with a K d value of aptamer CH1S-3 of 10.3 nM step2c_acs_v1
334 17 β -Estradiol protein P42167 22-mer aptamer   1.1000000000000001e-08 M -7.959 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   25803717 10.1021/acs.analchem.5b00335 new 35-mer and 22-mer aptamers were generated with K D ' s of 14 and 11 nM step2c_acs_v1
333 17 β -Estradiol protein P42167 35-mer aptamer   1.4000000000000001e-08 M -7.854 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   25803717 10.1021/acs.analchem.5b00335 new 35-mer and 22-mer aptamers were generated with K D ' s of 14 and 11 nM step2c_acs_v1
314 hMMP-9 protein   F3Bomf   2e-08 M -7.699 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     SPR 296.15   PBS buffer   2'-OMe-RNA 2'-O-methyl purine; 2'-fluoro pyrimidine; 5'-hexylamino linker; 5'-MAG3 conjugate 23043415 10.1021/bc300146c The K d was taken as the concentration leading to half saturation, i.e., about 20 nM. step2c_acs_v1
315 hMMP-9 protein   F3   2e-08 M -7.699 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp               2'F-RNA 2'-fluoro pyrimidine ribonucleosides 23043415 10.1021/bc300146c exhibits a strong a ffi nity for hMMP-9 ( K d = 20 nM) step2c_acs_v1
480 NMP22 protein Q14980 NT2a   2.4260000000000003e-08 M -7.615 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     MST         DNA biotin 42173503 10.1021/acs.analchem.6c00738 The K d values were also determined using MicroScale Thermophoresis (MST), and the K d values of NT2a and NT4a were determined to be 24.26 ± 10.47 and 77.29 ± 25.78 nM (Figures 2d and S3). step2c_acs_v1
321 S-adenosylmethionine protein P17707 Bs SAM-I riboswitch   2.5000000000000002e-08 M -7.602 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: 25 nM K d step2c_acs_v1
424 verrucarin A protein   Ver1_JYP   2.9500000000000003e-08 M -7.53 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   7.4 SELEX buffer   DNA   39404132 10.1021/acs.analchem.4c03307 The novel ssDNA aptamer exhibited a binding affinity of 29.5 nM step2c_acs_v1
325 L-TAR RNA protein Q13395 D-6-4t   3.0000000000000004e-08 M -7.523 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   23977945 10.1021/ja406634g The Kd of in vitro transcribed D-6-4t for L-TAR is 30 nM step2c_acs_v1
353 Thrombin protein P00734 Antithrombin aptamer   3.3000000000000004e-08 M -7.481 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   31580650 10.1021/acs.analchem.9b00081 Antithrombin aptamer with KD of 33 nM was successfully isolated by four rounds of MCP-SELEX. step2c_acs_v1
354 paramylon protein   Par-15   3.49e-08 M -7.457 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   7.5 binding buffer (50 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1 mM EDTA, pH 7.5)   DNA FAM 31809034 10.1021/acs.jafc.9b04588 The estimated K d values of fi ve selected aptamers, Par-7, Par-15, Par-18, Par-20, and Par-22, are 17.45 ± 2.61, 34.90 ± 5.83, 64.06 ± 6.72, 123.81 ± 13.41, and 249.52 ± 46.39 nM, respectively. step2c_acs_v1
311 HAP 1b protein   Aptamer 21   5.0000000000000004e-08 M -7.301 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   21899290 10.1021/nn2006927 A high-affinity RNA aptamer (K d = 50 nM) was efficiently identified by SELEX against a heteroaryl dihydropyrimidine structure step2c_acs_v1
355 paramylon protein   Par-18   6.406e-08 M -7.193 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   7.5 binding buffer (50 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1 mM EDTA, pH 7.5)   DNA FAM 31809034 10.1021/acs.jafc.9b04588 The estimated K d values of fi ve selected aptamers, Par-7, Par-15, Par-18, Par-20, and Par-22, are 17.45 ± 2.61, 34.90 ± 5.83, 64.06 ± 6.72, 123.81 ± 13.41, and 249.52 ± 46.39 nM, respectively. step2c_acs_v1
400 6'-sialyllactose protein Q9Y3R4 Apt9-1   9.175000000000001e-08 M -7.037 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence 298.15 7.4 10 mM PBS (pH 7.4)   DNA   36700646 10.1021/acs.jafc.2c07784 A 35 nt truncated aptamer Apt9-1 ( K d = 91.75 nM) with higher affinity than Apt9 was finally obtained. step2c_acs_v1
420 17 β -estradiol protein P42167 HEV1   9.276e-08 M -7.033 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     MST   7.6 20 mM Tris (pH 7.6), 300 mM NaCl, 5 mM MgCl2, 0.01% Tween 20   DNA   38276613 10.3390/molecules29020535 the dissociation constant (KD value) is 92.76 ± 66.02 nM as calculated by the calculation function that comes with the system. step2c_acs_v1
324 D-TAR RNA protein Q9Y5S9 L-6-4t   1.0000000000000001e-07 M -7.0 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   23977945 10.1021/ja406634g the K d of the L-aptamer for D-TAR RNA is 100 nM step2c_acs_v1
436 SIRT2 protein Q8IXJ6 Apt 45   1.233e-07 M -6.909 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence 310.15       DNA FAM 40200675 10.1021/acs.analchem.5c00066 selected Apt 45 ( K d = 123.3 nM) to fabricate the 'turn-on' fluorescent biosensor step2c_acs_v1
399 6'-sialyllactose protein Q9Y3R4 Apt9   1.5230000000000003e-07 M -6.817 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence 298.15 7.4 10 mM PBS (pH 7.4)   DNA   36700646 10.1021/acs.jafc.2c07784 The ssDNA aptamer Apt9 ( K d = 152.3 nM) with a length of 79 nucleotides (nt) was demonstrated as the optimal aptamer candidate step2c_acs_v1
326 D-TAR RNA protein Q9Y5S9 L-6-4t   1.6e-07 M -6.796 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   23977945 10.1021/ja406634g The L-6-4t aptamer has somewhat reduced affinity for D-TAR RNA under the low-salt conditions (K d = 160 nM) step2c_acs_v1
369 Cd2+ protein P06729 probe   2.2e-07 M -6.658 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp                   32618180 10.1021/acs.analchem.0c01710 the disassociation constant ( K D) between Cd 2+ and its aptamer were calculated to be 96 M -1 S -1 , 2.11 × 10 -5 S -1 , and 220 nM, respectively step2c_acs_v1
467 benzovindiflupyr protein   Apt.BZF01   2.2650000000000002e-07 M -6.645 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence         DNA   41614999 10.1021/acs.jafc.5c15044 corrected KDs of 226.5 nM (Apt.BZF01) step2c_acs_v1
425 verrucarin A protein   14_Ver1   2.2e-06 M -5.658 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   7.4 SELEX buffer   DNA 6-FAM at 5'-end; dabcyl at 3'-end 39404132 10.1021/acs.analchem.4c03307 The binding test demonstrated that the decrease in fluorescence was correlated with increasing verrucarin A concentration with K D = 2.2 μM. step2c_acs_v1
426 verrucarin A protein   Ver1_JYP (C32G mutant)   2.2999999999999996e-06 M -5.638 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   7.4 SELEX buffer   DNA C32G mutation 39404132 10.1021/acs.analchem.4c03307 guanine with both functional groups exhibited partially recovered binding activity ( K D = 2.3 μM). step2c_acs_v1
462 Patulin protein   PTL-1   1.2499999999999999e-05 M -4.903 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     ITC 298.15 6.0 selection buffer (10 mM MES, pH 6.0, 150 mM NaCl, 5 mM MgCl2)   DNA   41473783 10.1186/s44280-025-00101-2 The measured K d from ITC value was 12.5 μM step2c_acs_v1
463 Patulin protein   PTL-1   1.8399999999999997e-05 M -4.735 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   6.0 selection buffer (10 mM MES, pH 6.0, 150 mM NaCl, 5 mM MgCl2)   DNA   41473783 10.1186/s44280-025-00101-2 yielding an apparent K d of 18.4 μM step2c_acs_v1
388 patulin protein   PAT Rep   4e-05 M -4.398 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     SPR     PBS   DNA 5' biotin 35546052 10.1021/acs.jafc.2c01591 PAT Rep showed a K D value of 4.0 × 10 -5 M step2c_acs_v1
464 Patulin protein   PAT-6   4.8e-05 M -4.319 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence   6.0 20 mM MES buffer, pH = 6.0, with 150 mM NaCl and 2.0 mM MgCl2   DNA   41473783 10.1186/s44280-025-00101-2 PAT-6 has weaker binding affinities ( Kd = 48 μM by ThT, Fig. 4S) step2c_acs_v1
470 L-lactate protein Q9BYZ2 Lac2059   0.00011 M -3.959 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     ITC 298.15   SELEX buffer   DNA   41779931 10.1021/acs.analchem.5c07149 The K d from ITC was determined to be 0.11 mM step2c_acs_v1
471 L-lactate protein Q9BYZ2 Lac201   0.0009000000000000001 M -3.046 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence 296.15   SELEX buffer   DNA 2AP 41779931 10.1021/acs.analchem.5c07149 the fitted K d was 0.9 mM (Figure 5C, black line) step2c_acs_v1
457 Tris(hydroxymethyl)aminomethane protein   Tris aptamer   0.0026000000000000003 M -2.585 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence         DNA   40905906 10.1021/acs.analchem.5c03351 ThT yielded K d values changed modestly from 1.6 to 2.6 mM step2c_acs_v1
473 L-lactate protein Q9BYZ2 Lac2059   0.0033 M -2.481 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence 296.15   SELEX buffer   DNA 2AP 41779931 10.1021/acs.analchem.5c07149 The fitted K d was 3.3 mM for this 2AP-labeled aptamer step2c_acs_v1
472 L-lactate protein Q9BYZ2 Lac201   0.0043 M -2.367 intrinsic Kd Gold v4 multi_agent_verified pending_manual_supp     fluorescence 296.15   SELEX buffer   DNA 2AP 41779931 10.1021/acs.analchem.5c07149 although the obtained K d (4.3 mM) was about 5-fold higher than that obtained using Mg 2+ . step2c_acs_v1

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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';