Ligand profile

ZINC1553

Virtual-screening candidate from ZINC.

Bound to: VK055_4925 — apurinic endonuclease family protein

Via homolog UniProt P0A6C1 Formula C₁₃H₁₂N₄O
Tanimoto 1.00
Mol. weight 240.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1553
UniProt (similar protein)
P0A6C1
Tanimoto
1.000
Target protein
VK055_4925

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 240.27 Da
LogP (Crippen) 1.49
H-bond donors 1
H-bond acceptors 4
TPSA 59.28 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.15
Formula C₁₃H₁₂N₄O

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.

  • TPSA ≤ 90 Ų 59.3
  • −1 ≤ LogP ≤ 5 1.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 240.3
  • LogP ≤ 5 1.49
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 59.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C1CCC(c2ccc(-n3ccnc3)cc2)=NN1
InChI 
InChI=1S/C13H12N4O/c18-13-6-5-12(15-16-13)10-1-3-11(4-2-10)17-8-7-14-9-17/h1-4,7-9H,5-6H2,(H,16,18)
InChIKey 
VXMYWVMXSWJFCV-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
CHEMBL12831
Homolog
P0A6C1

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4925.

PDB 1

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

Ligand PDB entry

ChEMBL 64

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)