Ligand profile

U9V

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

Bound to: KP13_20485 — Cytochrome o ubiquinol oxidase subunit 3

Via homolog PDB 6wti UniProt P0ABJ3 Formula C₃₃H₆₄O₄
Mol. weight 524.87 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U9V
PDB
6wti
UniProt (similar protein)
P0ABJ3
Target protein
KP13_20485

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 524.87 Da
LogP (Crippen) 10.65
H-bond donors 0
H-bond acceptors 4
TPSA 52.60 Ų
Rotatable bonds 30
Aromatic rings 0 / 0
Heavy atoms 37
Fraction sp³ C 0.94
Formula C₃₃H₆₄O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 52.6
  • −1 ≤ LogP ≤ 5 10.65
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 524.9
  • LogP ≤ 5 10.65
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 30
  • TPSA ≤ 140 Ų 52.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OCCOC(=O)CCCCCCCCCCCCCC
InChI 
InChI=1S/C33H64O4/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-33(35)37-31-30-36-32(34)28-26-24-22-20-18-16-14-12-10-8-6-4-2/h3-31H2,1-2H3
InChIKey 
VKLOIKIKCDJYHU-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00115

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_20485.

PDB 29

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)