Ligand profile

3VR

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

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

Via homolog PDB 4wyd UniProt P9WQ81 Formula C₁₂H₁₅N₃
Mol. weight 201.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3VR
PDB
4wyd
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 201.27 Da
LogP (Crippen) 1.65
H-bond donors 1
H-bond acceptors 3
TPSA 29.85 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.25
Formula C₁₂H₁₅N₃

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 29.9
  • −1 ≤ LogP ≤ 5 1.65
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 201.3
  • LogP ≤ 5 1.65
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 29.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNCc1ccc(cc1)Cn2cccn2
InChI 
InChI=1S/C12H15N3/c1-13-9-11-3-5-12(6-4-11)10-15-8-2-7-14-15/h2-8,13H,9-10H2,1H3
InChIKey 
BQLXMVISWVMAID-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)