Ligand profile

G3X

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

Bound to: VK055_0532 — alpha/beta hydrolase fold family protein

Via homolog PDB 3i6m UniProt P04058 Formula C₂₄H₃₄N₂O₃
Mol. weight 398.55 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
G3X
PDB
3i6m
UniProt (similar protein)
P04058
Target protein
VK055_0532

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 398.55 Da
LogP (Crippen) 3.10
H-bond donors 1
H-bond acceptors 5
TPSA 45.17 Ų
Rotatable bonds 5
Aromatic rings 1 / 5
Heavy atoms 29
Fraction sp³ C 0.67
Formula C₂₄H₃₄N₂O₃

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 45.2
  • −1 ≤ LogP ≤ 5 3.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 398.5
  • LogP ≤ 5 3.10
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 45.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c3c1O[C@@H]4[C@@]3(CC[N@](C2)CCCN5CCCCC5)C=C[C@@H](C4)O
InChI 
InChI=1S/C24H34N2O3/c1-28-20-7-6-18-17-26(14-5-13-25-11-3-2-4-12-25)15-10-24-9-8-19(27)16-21(24)29-23(20)22(18)24/h6-9,19,21,27H,2-5,10-17H2,1H3/t19-,21-,24-/m0/s1
InChIKey 
JIMPGPISVDHAIE-PTLVVNQVSA-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
PF00135

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_0532.

PDB 16

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)