Binder profile

ZINC1637602

Virtual-screening candidate from ZINC.

Bound to: PA5304 — D-amino acid dehydrogenase small subunit

Via homolog UniProt Q50LF2 C21H25N5O6

Tanimoto 0.60

Mol. weight 443.46 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC1637602
UniProt (similar protein): Q50LF2
Tanimoto: 0.600
Target protein: PA5304

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.46 Da

LogP (Crippen) 0.62

H-bond donors 6

H-bond acceptors 7

TPSA 187.50 Å²

Rotatable bonds 9

Aromatic rings 2 / 3

Heavy atoms 32

Fraction sp³ C 0.38

Formula C21H25N5O6

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

Lipinski's Rule of Five Pass 1 violation

MW ≤ 500 Da 443.5
LogP ≤ 5 0.62
H-bond donors ≤ 5 6
H-bond acceptors ≤ 10 7

Veber's rules Fail

Rotatable bonds ≤ 10 9
TPSA ≤ 140 Å² 187.5

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

Nc1nc(=O)c2c([nH]1)NC[C@@H](CCc1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1)C2

InChI

InChI=1S/C21H25N5O6/c22-21-25-17-14(19(30)26-21)9-12(10-23-17)2-1-11-3-5-13(6-4-11)18(29)24-15(20(31)32)7-8-16(27)28/h3-6,12,15H,1-2,7-10H2,(H,24,29)(H,27,28)(H,31,32)(H4,22,23,25,26,30)/t12-,15-/m0/s1

InChIKey

ZUQBAQVRAURMCL-WFASDCNBSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method: LigQ nearest_k
Query: FON
Homolog: Q50LF2

External resources

Open this ligand in third-party databases and cheminformatics tools.

ZINC ZINC15 ZINC1637602 →
ZINC ZINC20 ZINC1637602 →
UniProt UniProt Q50LF2 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC1637602”) →

Other binders for this protein

Quick navigation to other ligands bound to PA5304.

PDB 9

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)