Binder profile

ZINC8628601

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q50LF2 C21H27N7O6

Tanimoto 0.72

Mol. weight 473.49 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC8628601
UniProt (similar protein): Q50LF2
Tanimoto: 0.716
Target protein: PA5304

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 473.49 Da

LogP (Crippen) 0.13

H-bond donors 7

H-bond acceptors 9

TPSA 202.77 Å²

Rotatable bonds 10

Aromatic rings 2 / 3

Heavy atoms 34

Fraction sp³ C 0.38

Formula C21H27N7O6

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 473.5
LogP ≤ 5 0.13
H-bond donors ≤ 5 7
H-bond acceptors ≤ 10 9

Veber's rules Fail

Rotatable bonds ≤ 10 10
TPSA ≤ 140 Å² 202.8

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1

InChI

InChI=1S/C21H27N7O6/c1-28-13(10-24-17-16(28)19(32)27-21(22)26-17)8-9-23-12-4-2-11(3-5-12)18(31)25-14(20(33)34)6-7-15(29)30/h2-5,13-14,23H,6-10H2,1H3,(H,25,31)(H,29,30)(H,33,34)(H4,22,24,26,27,32)/t13-,14+/m1/s1

InChIKey

KCPBTDJBDDCNQE-KGLIPLIRSA-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 ZINC8628601 →
ZINC ZINC20 ZINC8628601 →
UniProt UniProt Q50LF2 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC8628601”) →

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)