Ligand profile

3G9

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

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

Via homolog PDB 4w1x UniProt P9WQ80 Formula C₁₉H₁₉ClN₂O₂
Mol. weight 342.83 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3G9
PDB
4w1x
UniProt (similar protein)
P9WQ80
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 342.83 Da
LogP (Crippen) 3.51
H-bond donors 0
H-bond acceptors 3
TPSA 40.62 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.26
Formula C₁₉H₁₉ClN₂O₂

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 40.6
  • −1 ≤ LogP ≤ 5 3.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 342.8
  • LogP ≤ 5 3.51
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 40.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3cccc(c3)Cl
InChI 
InChI=1S/C19H19ClN2O2/c1-14(23)15-5-7-18(8-6-15)21-9-11-22(12-10-21)19(24)16-3-2-4-17(20)13-16/h2-8,13H,9-12H2,1H3
InChIKey 
RCHDWCNBGCYJNK-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)