Protein target profile
KP13_31803
glycine cleavage system aminomethyltransferase T
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Terms and data sources used on this page
PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.
AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.
ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.
pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.
FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.
Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.
PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.
ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.
ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.
LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.
Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.
DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.
Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.
EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.
KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.
Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.
Prioritization evidence
Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.
Off-target risk
- Human off-target
- Hit
- Human identity (%)
- 34.191 Lower values reduce human off-target concern.
- Human E-value
- 1.99e-39
- Gut microbiome similarity
- 3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 0.0 Higher values support similarity to known essential genes.
Localization
- Localization
- Cytoplasmic
Structure confidence
- ColabFold pLDDT
- 95.98 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MAGSVLFDEEKMAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRIREFLRYLLANDVAKLTTPGKALYTGMLTASAGVIDDLIVYFLSEDYFRLVVNSATREKDLAWISEQAEPYGLEITVRDDLSLIAVQGPQAKAKAATLFTDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIAMPNEQAADFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEMDEGVSPLAANMGWTIAWEPADRNFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRFTDSDGNQKEGIITSGTFSPTLGYSIALARVPAGIGDTAVVQIRNREMPVKVTKPGFVRNGKAIV
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
3- GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine.
- GO:0005515 Binding to a protein.
- GO:0004047 Catalysis of the reaction: N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4+.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 288 | 375 | Gene3D | G3DSA:2.40.30.110 | - |
| 18 | 265 | Pfam | PF01571 | Aminomethyltransferase folate-binding domain |
| 18 | 265 | InterPro | IPR006222 | Aminomethyltransferase, folate-binding domain |
| 282 | 372 | SUPERFAMILY | SSF101790 | Aminomethyltransferase beta-barrel domain |
| 282 | 372 | InterPro | IPR029043 | Glycine cleavage T-protein/YgfZ, C-terminal |
| 16 | 242 | Gene3D | G3DSA:3.30.1360.120 | Probable tRNA modification gtpase trme; domain 1 |
| 16 | 242 | InterPro | IPR027266 | GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 |
| 243 | 287 | Gene3D | G3DSA:4.10.1250.10 | Aminomethyltransferase fragment |
| 4 | 374 | PIRSF | PIRSF006487 | GCST |
| 243 | 287 | FunFam | G3DSA:4.10.1250.10:FF:000001 | Aminomethyltransferase |
| 12 | 370 | PANTHER | PTHR43757 | AMINOMETHYLTRANSFERASE |
| 12 | 370 | InterPro | IPR028896 | Aminomethyltransferase-like |
| 62 | 150 | FunFam | G3DSA:3.30.70.1400:FF:000001 | Aminomethyltransferase |
| 288 | 375 | FunFam | G3DSA:2.40.30.110:FF:000001 | Aminomethyltransferase |
| 13 | 370 | NCBIfam | TIGR00528 | glycine cleavage system aminomethyltransferase GcvT |
| 13 | 370 | InterPro | IPR006223 | Glycine cleavage system T protein |
| 12 | 370 | Hamap | MF_00259 | Aminomethyltransferase [gcvT]. |
| 12 | 370 | InterPro | IPR022903 | Glycine cleavage system T protein, bacteria |
| 14 | 288 | SUPERFAMILY | SSF103025 | Folate-binding domain |
| 291 | 367 | Pfam | PF08669 | Glycine cleavage T-protein C-terminal barrel domain |
| 291 | 367 | InterPro | IPR013977 | Glycine cleavage T-protein, C-terminal barrel domain |
| 62 | 149 | Gene3D | G3DSA:3.30.70.1400 | - |
3D structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
All structural evidence
Structural evidence
0 + 2Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold DB
AF_A0A0H3H2N5
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_31803
|
ColabFold | — | — | full sequence | — | Loaded |
Ligand evidence
Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| C2F RCSB PDB | P27248 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…
|
|
| FFO RCSB PDB | Q9WY54 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…
|
|
| FOA RCSB PDB | Q3ZDQ8 | 112.1 Da LogP 0.98 TPSA 50.4 | ✓ Ro5 | ✓ Clean |
c1cc(oc1)C(=O)O
|
|
| RED RCSB PDB | Q9WY54 | 208.3 Da LogP 2.25 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
C(CCC(=O)O)C[C@H](CCS)S
|
|
| THG RCSB PDB | Q63342 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1529363 ZINC | 1.000 | 208.3 Da LogP 2.25 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@H](S)CCS
|
| ZINC2572666 ZINC | 1.000 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…
|
| ZINC3869601 ZINC | 1.000 | 208.3 Da LogP 2.25 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@@H](S)CCS
|
| ZINC4228235 ZINC | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…
|
| ZINC4228236 ZINC | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…
|
| ZINC4228237 ZINC | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…
|
| ZINC4228238 ZINC | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…
|
| ZINC8618631 ZINC | 0.848 | 459.5 Da LogP 0.11 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H]…
|
| ZINC8627114 ZINC | 0.848 | 459.5 Da LogP 0.11 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)N[C@@H…
|
| ZINC4228247 ZINC | 0.712 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CN(C=O)c1ccc(C(=O)N[C…
|
| ZINC2005305 ZINC | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…
|
| ZINC4228266 ZINC | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…
|
| ZINC4228267 ZINC | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…
|
| ZINC9212425 ZINC | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…
|
| ZINC9212426 ZINC | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…
|
| ZINC9212427 ZINC | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…
|
| ZINC9212428 ZINC | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…
|
| ZINC85394426 ZINC | 0.667 | 206.2 Da LogP 1.80 TPSA 80.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccco2)o1
|
| ZINC8618632 ZINC | 0.635 | 459.5 Da LogP 0.52 TPSA 211.8 | 1 viol. | ✓ Clean |
Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@H](CC…
|
| ZINC8627115 ZINC | 0.635 | 459.5 Da LogP 0.52 TPSA 211.8 | 1 viol. | ✓ Clean |
Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC…
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| ZINC4228265 ZINC | 0.630 | 443.4 Da LogP 0.01 TPSA 211.9 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@@H](CCC…
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| ZINC4517559 ZINC | 0.630 | 443.4 Da LogP 0.01 TPSA 211.9 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@H](CCC(…
|
| ZINC12374887 ZINC | 0.630 | 216.2 Da LogP 2.21 TPSA 67.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccco2)cc1
|
| ZINC8655682 ZINC | 0.628 | 487.5 Da LogP -0.34 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…
|
| ZINC13887836 ZINC | 0.616 | 429.4 Da LogP 0.54 TPSA 187.5 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)[C@@H](CCc1ccc(C(=O)N[C@@H](…
|
| ZINC1710770 ZINC | 0.615 | 200.2 Da LogP 2.35 TPSA 47.3 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccco1)c1ccccc1
|
| ZINC4658141 ZINC | 0.608 | 443.5 Da LogP 0.62 TPSA 187.5 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)C[C@H](CCc1ccc(C(=O)N[C@H](C…
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| ZINC4658144 ZINC | 0.608 | 443.5 Da LogP 0.62 TPSA 187.5 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)C[C@@H](CCc1ccc(C(=O)N[C@H](…
|
| ZINC1613560 ZINC | 0.607 | 216.2 Da LogP 2.21 TPSA 67.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)c1ccco1
|
| ZINC4228269 ZINC | 0.605 | 456.4 Da LogP -0.61 TPSA 193.7 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…
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| ZINC4228270 ZINC | 0.605 | 456.4 Da LogP -0.61 TPSA 193.7 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…
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| ZINC100477623 ZINC | 0.600 | 204.2 Da LogP 2.33 TPSA 60.4 | ✓ Ro5 | ✓ Clean |
O=C(CC(=O)c1ccco1)c1ccco1
|
| ZINC6472822 ZINC | 0.600 | 218.2 Da LogP 2.72 TPSA 60.4 | ✓ Ro5 | ✓ Clean |
O=C(CCC(=O)c1ccco1)c1ccco1
|
| ZINC156403 ZINC | 0.593 | 274.3 Da LogP 1.47 TPSA 66.9 | ✓ Ro5 | ✓ Clean |
O=C(c1ccco1)N1CCN(C(=O)c2ccco2)CC1
|
| ZINC4654270 ZINC | 0.592 | 471.4 Da LogP -0.36 TPSA 211.0 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…
|
| ZINC4654271 ZINC | 0.592 | 471.4 Da LogP -0.36 TPSA 211.0 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…
|
| ZINC13515262 ZINC | 0.589 | 439.4 Da LogP 1.17 TPSA 187.5 | 1 viol. | ✓ Clean |
Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…
|
| ZINC4228243 ZINC | 0.584 | 457.4 Da LogP -0.52 TPSA 194.0 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…
|
| ZINC4228244 ZINC | 0.584 | 457.4 Da LogP -0.52 TPSA 194.0 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@H](CCC(=…
|
| ZINC4654260 ZINC | 0.584 | 457.4 Da LogP -0.52 TPSA 194.0 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…
|
| ZINC8664075 ZINC | 0.580 | 330.3 Da LogP 0.76 TPSA 145.2 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)O)cc1)…
|
| ZINC983943 ZINC | 0.577 | 360.3 Da LogP 4.16 TPSA 90.6 | ✓ Ro5 | ✓ Clean |
O=C(c1cc(C(=O)c2ccco2)cc(C(=O)c2ccco2)c1)c1ccco1
|
| ZINC77301924 ZINC | 0.573 | 443.4 Da LogP 0.07 TPSA 204.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)[C@H](CCc1ccc(C(=O)N[C@H](CC…
|
| ZINC106891773 ZINC | 0.571 | 204.2 Da LogP 2.65 TPSA 63.6 | ✓ Ro5 | ✓ Clean |
O=C(/C=C(\O)c1ccco1)c1ccco1
|
| ZINC1567048 ZINC | 0.568 | 440.4 Da LogP 0.56 TPSA 200.4 | 1 viol. | ✓ Clean |
Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…
|
| ZINC1995991 ZINC | 0.568 | 439.4 Da LogP 1.17 TPSA 187.5 | 1 viol. | ✓ Clean |
Nc1nc2ccc(NCc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…
|
| ZINC200768381 ZINC | 0.568 | 344.3 Da LogP -0.08 TPSA 153.4 | ✓ Ro5 | ✓ Clean |
Nc1nc(=O)c2c([nH]1)NC[C@@H](CNc1ccc(C(=O)O)cc1)…
|
| ZINC200768411 ZINC | 0.568 | 344.3 Da LogP -0.08 TPSA 153.4 | ✓ Ro5 | ✓ Clean |
Nc1nc(=O)c2c([nH]1)NC[C@H](CNc1ccc(C(=O)O)cc1)N…
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| ZINC49815930 ZINC | 0.567 | 216.2 Da LogP 2.21 TPSA 67.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(C(=O)c2ccco2)c1
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| ZINC1560405340 ZINC | 0.561 | 472.4 Da LogP -0.16 TPSA 220.1 | 1 viol. | ✓ Clean |
Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C](CCC(=O…
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PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.