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).

9 rows where sequence_status = "pending_manual_figure", tier = "Gold" and verification_level = "multi_agent_verified" sorted by kd_log10_molar

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Suggested facets: target_name_canonical, target_uniprot, aptamer_name, source_pmid, doi

measurement_class 2

verification_level 1

  • multi_agent_verified · 9 ✖

tier 1

  • Gold · 9 ✖

target_type 1

sequence_status 1

  • pending_manual_figure · 9 ✖

binding_constant_type 1

assay_method 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
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
336 VEGF-165 protein P15692 bivalent construct for VEGF-165 (no linker)   1.7e-08 M -7.77 avidity_multivalent Kd Gold v4 multi_agent_verified pending_manual_figure                   27043498 10.3390/molecules21040421 this bivalent construct had about 28-fold higher binding affinity ( K D = 17 nM) step2c_acs_v1
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
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

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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';