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).

15 rows where measurement_class = "non_intrinsic" and target_type = "cell/EV" sorted by kd_log10_molar

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

assay_method 3

sequence_status 2

verification_level 1

tier 1

target_type 1

  • cell/EV · 15 ✖

measurement_class 1

  • non_intrinsic · 15 ✖

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
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
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
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
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
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
302 prostate-cancer-derived small extracellular vesicles cell/EV Q99523 seq25   24.02 nM -7.619 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     SPR     PBST buffer   DNA 5'-FAM 41646885 10.1016/j.omtn.2026.102836 The affinity of seq25 for positive selection was significantly higher than that of the other aptamers, with a KD of 24.02 nM step2c_literal_v3
207 SW480 cells cell/EV Q16520 SYL3C   142.5 nM -6.846 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA cholesterol 32049531 10.1021/jacs.9b13782 monovalent SYL3C aptamer ( K d = 142.50 ± 20.55 nM, Figure 2A) step2c_literal_v3
263 H-6 cells cell/EV O14756 Apta25   0.42 µM -6.377 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 H-6 cells showed binding with Apta25 ( K D value-0.42 ± 0.093 µ m) step2c_literal_v3
261 K-1 cells cell/EV O60814 Apta30   0.66 µM -6.18 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 Apta30 ( K D -0.66 ± 0.12 µ m) step2c_literal_v3
264 H-6 cells cell/EV O14756 Apta30   1.107 µM -5.956 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 H-6 cells showed binding with ... Apta30 ( K D -1.107 ± 0.208 µ m) step2c_literal_v3
262 K-1 cells cell/EV O60814 Apta25   1.358 µM -5.867 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 Apta25 ( K D value-1.358 ± 0.201 µ m) step2c_literal_v3
259 K-1 cells cell/EV O60814 Apta02   1.821 µM -5.74 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 Apta02 ( K D value-1.821 ± 0.117 µ m) step2c_literal_v3
260 K-1 cells cell/EV O60814 Apta04   1.867 µM -5.729 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 Apta04 ( K D value-1.867 ± 0.19 µ m) step2c_literal_v3
265 H-9 cells cell/EV Q8IVB4 Apta02   4.93 µM -5.307 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 H-9 cells showed binding with Apta02 ( K D value-4.93 ± 0.367 µ m) step2c_literal_v3
266 H-9 cells cell/EV Q8IVB4 Apta04   5.402 µM -5.267 non_intrinsic Kd Gold v4 extraction_verified pending_supp_oa     flow_cytometry 310.15       DNA   40487293 10.1002/adfm.202425394 H-9 cells showed binding with ... Apta04 ( K D value-5.402 ± 0.795 µ m) 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';