Ligand profile

ZINC58633440

Virtual-screening candidate from ZINC.

Bound to: VK055_2468 — 8-oxo-dGTPase

Via homolog UniProt A0R2K6 Formula C₉H₁₇N₄O₁₃P₃
Tanimoto 0.69
Mol. weight 482.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC58633440
UniProt (similar protein)
A0R2K6
Tanimoto
0.695
Target protein
VK055_2468

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 482.17 Da
LogP (Crippen) -2.25
H-bond donors 7
H-bond acceptors 13
TPSA 276.21 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.56
Formula C₉H₁₇N₄O₁₃P₃

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 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 276.2
  • −1 ≤ LogP ≤ 5 -2.25
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 482.2
  • LogP ≤ 5 -2.25
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 276.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)[C@@H](O)[C@H]2N)c(=O)n1
InChI 
InChI=1S/C9H17N4O13P3/c10-5-1-2-13(9(15)12-5)8-6(11)7(14)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,14H,3,11H2,(H,19,20)(H,21,22)(H2,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKey 
WNVZQYHBHSLUHJ-XVFCMESISA-N

Provenance

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

Method
LigQ nearest_k
Query
DCP
Homolog
A0R2K6

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_2468.

PDB 6

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)