Ligand profile

9L3

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

Bound to: VK055_2468 — 8-oxo-dGTPase

Via homolog PDB 5zri UniProt A0R2K6 Formula C₁₀H₁₇N₃O₆P⁺
Mol. weight 306.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9L3
PDB
5zri
UniProt (similar protein)
A0R2K6
Target protein
VK055_2468

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 306.23 Da
LogP (Crippen) -0.98
H-bond donors 4
H-bond acceptors 6
TPSA 139.01 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 20
Fraction sp³ C 0.60
Formula C₁₀H₁₇N₃O₆P⁺

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 139.0
  • −1 ≤ LogP ≤ 5 -0.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 306.2
  • LogP ≤ 5 -0.98
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 139.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c[n+](cnc1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
InChI 
InChI=1S/C10H16N3O6P/c1-6-3-13(5-12-10(6)11)9-2-7(14)8(19-9)4-18-20(15,16)17/h3,5,7-9,11,14H,2,4H2,1H3,(H2,15,16,17)/p+1/t7-,8+,9+/m0/s1
InChIKey 
RJJVNUWWHKQVPB-DJLDLDEBSA-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)