Ligand profile

3VX

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

Bound to: VK055_1732 — adenosylmethionine-8-amino-7-oxononanoate transaminase

Via homolog PDB 4wyf UniProt P9WQ81 Formula C₁₁H₉NO₂
Mol. weight 187.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3VX
PDB
4wyf
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 187.20 Da
LogP (Crippen) 1.85
H-bond donors 1
H-bond acceptors 2
TPSA 46.17 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 14
Fraction sp³ C 0.09
Formula C₁₁H₉NO₂

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 46.2
  • −1 ≤ LogP ≤ 5 1.85
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 187.2
  • LogP ≤ 5 1.85
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 46.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)Nc1ccc2c(c1)C=CC2=O
InChI 
InChI=1S/C11H9NO2/c1-7(13)12-9-3-4-10-8(6-9)2-5-11(10)14/h2-6H,1H3,(H,12,13)
InChIKey 
IBLLSZUYVXWELO-UHFFFAOYSA-N

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
PF00202

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_1732.

PDB 25

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

Ligand PDB entry

ChEMBL 100

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)