Binder profile

ZINC6472822

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q3ZDR0 C12H10O4
Tanimoto 0.60
Mol. weight 218.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC6472822
UniProt (similar protein)
Q3ZDR0
Tanimoto
0.600
Target protein
PA5304

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.21 Da
LogP (Crippen) 2.72
H-bond donors 0
H-bond acceptors 4
TPSA 60.42 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.17
Formula C12H10O4

Drug-likeness

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

Permeability proxy High

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

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.2
  • LogP ≤ 5 2.72
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 60.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(CCC(=O)c1ccco1)c1ccco1
InChI 
InChI=1S/C12H10O4/c13-9(11-3-1-7-15-11)5-6-10(14)12-4-2-8-16-12/h1-4,7-8H,5-6H2
InChIKey 
YFFKNPBNZUAMNU-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
FOA
Homolog
Q3ZDR0

External resources

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

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)