Ligand profile

523

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_2468 — 8-oxo-dGTPase

Via homolog PDB 5zro UniProt A0R2K6 Formula C₁₀H₁₉N₃O₁₃P₃⁺
Mol. weight 482.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
523
PDB
5zro
UniProt (similar protein)
A0R2K6
Target protein
VK055_2468

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 482.19 Da
LogP (Crippen) -1.46
H-bond donors 7
H-bond acceptors 10
TPSA 252.04 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.60
Formula C₁₀H₁₉N₃O₁₃P₃⁺

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 252.0
  • −1 ≤ LogP ≤ 5 -1.46
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 482.2
  • LogP ≤ 5 -1.46
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 252.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(NC(=O)[N+](=C1)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)N
InChI 
InChI=1S/C10H18N3O13P3/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,14H,2,4H2,1H3,(H6,11,12,15,16,17,18,19,20,21,22)/p+1/t6-,7+,8+/m0/s1
InChIKey 
VSWHQKSDLZFLRY-XLPZGREQSA-O

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00293

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 5

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)