Ligand profile

3VS

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

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

Via homolog PDB 4wyc UniProt P9WQ81 Formula C₁₀H₉N₃O
Mol. weight 187.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3VS
PDB
4wyc
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) 0.97
H-bond donors 1
H-bond acceptors 3
TPSA 60.91 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.00
Formula C₁₀H₉N₃O

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 60.9
  • −1 ≤ LogP ≤ 5 0.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 187.2
  • LogP ≤ 5 0.97
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 60.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)N)n2ccnc2
InChI 
InChI=1S/C10H9N3O/c11-10(14)8-1-3-9(4-2-8)13-6-5-12-7-13/h1-7H,(H2,11,14)
InChIKey 
VEKNMVRNEBNHNU-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)