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).

31 rows where measurement_class = "non_intrinsic", sequence_status = "pending_manual_supp" and tier = "Gold" sorted by kd_log10_molar

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Suggested facets: target_name_canonical, target_uniprot, aptamer_name, kd_reported, kd_log10_molar, assay_temperature_k, assay_ph, assay_buffer, assay_cations, aptamer_modifications, source_pmid, doi, verbatim_quote

target_type 2

verification_level 1

tier 1

  • Gold · 31 ✖

sequence_status 1

  • pending_manual_supp · 31 ✖

measurement_class 1

  • non_intrinsic · 31 ✖

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
188 PDGF-BB protein P01127 36aApt   0.036 pM -13.444 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 36aApt | 0.036 ± 0.012 | - 18.33 step2c_literal_v3
186 PDGF-BB protein P01127 38aApt   0.094 pM -13.027 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 38aApt | 0.094 ± 0.008 | - 17.76 step2c_literal_v3
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
184 PDGF-BB protein P01127 FullApt   5.33 pM -11.273 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 FullApt | 5.33 ± 2.36 | - 15.37 step2c_literal_v3
185 PDGF-BB protein P01127 40Apt   5.92 pM -11.228 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 40Apt | 5.92 ± 1.13 | - 15.31 step2c_literal_v3
187 PDGF-BB protein P01127 38bApt   7.03 pM -11.153 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     ELISA 298.0       DNA   28825469 10.1021/acscombsci.6b00163 38bApt | 7.03 ± 1.28 | - 15.21 step2c_literal_v3
269 thrombin protein P00734 HD1-12A-DAB   13.1 pM -10.883 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     filter_binding     selection buffer   DNA   41053535 10.1002/advs.202509867 HD1-12A-DAB EXACT inhibitor bound to thrombin and prothrombin with K D s of 13.1 pm 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
205 thrombin protein P00734 TBA29   0.5 nM -9.301 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA   31614078 10.1021/acs.analchem.9b03368 The 29-nt TBA29 aptamer has a bimodular duplex-antiparallel G4 structure and binds to thrombin with a binding a ffi nity of 0.5 nM. 30 step2c_literal_v3
303 EGFR protein P00533 Anti-EGF receptor aptamer   0.62 nM -9.208 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA 3' end sulfhydryl group (-SH) 41877526 10.1021/acs.molpharmaceut.5c01966 Anti-EGF receptor aptamers ( K d : 0.62 nM, DNA aptamers) 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
228 CD8 protein P01732 A3t   2.0 nM -8.699 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA   36149728 10.1021/acsami.2c11783 A3t, a CD8 receptor-binding aptamer, which binds CD8-expressing cells with an equilibrium dissociation constant K D of 2 nM. step2c_literal_v3
232 CD8 protein P01732 rvCD8apt   2.0 nM -8.699 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA 8 nt toehold 36149728 10.1021/acsami.2c11783 apparent K D = 2 nM for CD8 + cells step2c_literal_v3
211 K562 protein Q8WUY8 PAM   3.2 nM -8.495 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA FAM 32307868 10.1002/anie.202004206 the K d value (3.2 nM) of PAM in binding the K562 cell is one order of magnitude lower than that of the aptamer alone (41 nM). step2c_literal_v3
267 Thyroid-Stimulating Hormone Receptor (TSHR) 6X His tag protein   ZMXLY-2a   11.5 nM -7.939 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry     phosphate-buffered saline   DNA FITC-labeled 5' primer used for synthesis 40588369 10.1021/acs.analchem.5c02024 As determined by flow cytometry, the K d of ZMXLY-2a was 11.5 ± 9.3 nM (Figure 2G) step2c_literal_v3
183 human immunoglobulin E protein Q96D42 T40-AptIgE-3'-TMR   15.0 nM -7.824 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     CE-LIF 298.15 7.5 sample bu ff er containing 10 mM Tris-HCl (pH 7.5) and 1 mM MgCl2 1.0 DNA TMR label at 3'-end; polyT tail (40 T) at 5'-end 28763192 10.1021/acs.analchem.7b02313 The K d of T40-AptIgE-3 ′ -TMR was about 15 nM step2c_literal_v3
212 M2-like macrophage protein Q8IYS5 A2   22.81 nM -7.642 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry 277.15   Wash Buffer (WB) supplemented with 10% FBS and 100 μg/mL tRNA   DNA Cy5-label 32589412 10.1021/acs.bioconjchem.0c00247 apparent dissociation constants ( K d ) of 44.12 ± 8.0 and 22.81 ± 5.6 nM to M0- and M2-like macrophages, respectively step2c_literal_v3
210 K562 protein Q8WUY8 aptamer-FAM   41.0 nM -7.387 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp               DNA FAM 32307868 10.1002/anie.202004206 the K d value (3.2 nM) of PAM in binding the K562 cell is one order of magnitude lower than that of the aptamer alone (41 nM). step2c_literal_v3
257 CD71 protein P02786 XQ 2d   42.34 nM -7.373 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry     PBS supplemented with 0.5 mM MgCl2 and 0.05% BSA (BB buffer) 0.5 DNA FAM 40156524 10.1021/acs.analchem.5c00711 aptamers (HG1-9, K d = 43.23 ± 4.62 nM and XQ-2d, K d = 42.34 ± 5.15 nM)) step2c_literal_v3
258 CD71 protein P02786 HG1-9   43.23 nM -7.364 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry     PBS supplemented with 0.5 mM MgCl2 and 0.05% BSA (BB buffer) 0.5 DNA FAM 40156524 10.1021/acs.analchem.5c00711 aptamers (HG1-9, K d = 43.23 ± 4.62 nM and XQ-2d, K d = 42.34 ± 5.15 nM)) step2c_literal_v3
213 M0-like macrophage protein P01854 A2   44.12 nM -7.355 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry 277.15   Wash Buffer (WB) supplemented with 10% FBS and 100 μg/mL tRNA   DNA Cy5-label 32589412 10.1021/acs.bioconjchem.0c00247 apparent dissociation constants ( K d ) of 44.12 ± 8.0 and 22.81 ± 5.6 nM to M0- and M2-like macrophages, respectively step2c_literal_v3
214 monocyte protein P13500 A2   45.0 nM -7.347 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry 277.15   Wash Buffer (WB) supplemented with 10% FBS and 100 μg/mL tRNA   DNA Cy5-label 32589412 10.1021/acs.bioconjchem.0c00247 aptamer A2 bound CD14 + cells (monocytes) with high speci fi city ( K d ∼ 45 ± 9.1 nM) step2c_literal_v3
300 CD71 protein P02786 ATL   48.17 nM -7.317 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry 277.15 6.5 binding buffer   DNA Cy5-labeled; Cy3-labeled; Triplex motif 41412185 10.1021/acs.nanolett.5c04783 K(pH 6.5) = 48.17 ± 2.70 nM step2c_literal_v3
182 human immunoglobulin E protein Q96D42 AptIgE-3'-TMR   50.0 nM -7.301 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     CE-LIF 298.15 7.5 sample bu ff er containing 10 mM Tris-HCl (pH 7.5) and 1 mM MgCl2 1.0 DNA TMR label at 3'-end 28763192 10.1021/acs.analchem.7b02313 The apparent K d of AptIgE-3 ′ -TMR was about 50 nM step2c_literal_v3
268 Thyroid-Stimulating Hormone Receptor (TSHR) protein P16473 TSHRly-1c   54.37 nM -7.265 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry     binding buffer   DNA AlexaFluor 647-labeled 40588369 10.1021/acs.analchem.5c02024 As shown in Figure 4E, the apparent equilibrium dissociation constant ( K d) of TSHRly-1c was determined to be 54.37 ± 8.22 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
179 human α-thrombin protein P00734 T25-Apt15-3'-TMR   228.0 nM -6.642 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     CE-LIF 298.15 7.5 sample bu ff er containing 10 mM Tris-HCl (pH 7.5) and 5 mM KCl   DNA TMR label at 3'-end; polyT tail (25 T) at 5'-end 28763192 10.1021/acs.analchem.7b02313 The apparent K d values of T25-Apt15-3 ′ -TMR and 5 ′ -TMR-T25-Apt15 were estimated as 228 nM and 8.8 nM, respectively step2c_literal_v3
270 prothrombin protein P00734 HD1-12A-DAB   296.0 nM -6.529 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     filter_binding     selection buffer   DNA   41053535 10.1002/advs.202509867 and prothrombin with K D s of 13.1 pm and 296 nm step2c_literal_v3
301 CD71 protein P02786 ATL   696.7 nM -6.157 non_intrinsic Kd Gold v4 extraction_verified pending_manual_supp     flow_cytometry 277.15 7.5 binding buffer   DNA Cy5-labeled; Cy3-labeled; Triplex motif 41412185 10.1021/acs.nanolett.5c04783 K(pH 7.5)= 696.7 ± 68.03 nM 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';