Binder profile

ZINC4616626

Virtual-screening candidate from ZINC.

Bound to: PA2256 — paerucumarin biosynthesis protein PvcC

Via homolog UniProt Q53008 C13H11N3O3
Tanimoto 0.56
Mol. weight 257.25 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4616626
UniProt (similar protein)
Q53008
Tanimoto
0.562
Target protein
PA2256

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 257.25 Da
LogP (Crippen) 2.75
H-bond donors 2
H-bond acceptors 5
TPSA 87.76 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 19
Fraction sp³ C 0.00
Formula C13H11N3O3

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 257.2
  • LogP ≤ 5 2.75
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 87.8
PAINS Alert

Matches PAINS filter: hzone_phenol_B(215). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=[N+]([O-])c1ccc(N/N=C/c2ccc(O)cc2)cc1
InChI 
InChI=1S/C13H11N3O3/c17-13-7-1-10(2-8-13)9-14-15-11-3-5-12(6-4-11)16(18)19/h1-9,15,17H/b14-9+
InChIKey 
YLJOVQDNCKOFIN-NTEUORMPSA-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)