Binder profile

ZINC100009140

Virtual-screening candidate from ZINC.

Bound to: PA2256 — paerucumarin biosynthesis protein PvcC

Via homolog UniProt Q53008 C12H9N3O3
Tanimoto 0.75
Mol. weight 243.22 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC100009140
UniProt (similar protein)
Q53008
Tanimoto
0.750
Target protein
PA2256

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.22 Da
LogP (Crippen) 3.72
H-bond donors 1
H-bond acceptors 5
TPSA 88.09 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.00
Formula C12H9N3O3

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 243.2
  • LogP ≤ 5 3.72
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 88.1
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=[N+]([O-])c1ccc(/N=N/c2ccc(O)cc2)cc1
InChI 
InChI=1S/C12H9N3O3/c16-12-7-3-10(4-8-12)14-13-9-1-5-11(6-2-9)15(17)18/h1-8,16H/b14-13+
InChIKey 
NRJPVIOTANUINF-BUHFOSPRSA-N

Provenance

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

Method
LigQ nearest_k
Query
NPO
Homolog
Q53008

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2256.

PDB 3

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)