Ligand profile

PGV

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

Bound to: KP13_20485 — Cytochrome o ubiquinol oxidase subunit 3

Via homolog PDB 1v54 UniProt P00415 Formula C₄₀H₇₇O₁₀P
Mol. weight 749.02 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PGV
PDB
1v54
UniProt (similar protein)
P00415
Target protein
KP13_20485

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 749.02 Da
LogP (Crippen) 10.45
H-bond donors 3
H-bond acceptors 9
TPSA 148.82 Ų
Rotatable bonds 39
Aromatic rings 0 / 0
Heavy atoms 51
Fraction sp³ C 0.90
Formula C₄₀H₇₇O₁₀P

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 148.8
  • −1 ≤ LogP ≤ 5 10.45
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 749.0
  • LogP ≤ 5 10.45
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 39
  • TPSA ≤ 140 Ų 148.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OC[C@H](CO)O)OC(=O)CCCCCCCCC\C=C/CCCCCC
InChI 
InChI=1S/C40H77O10P/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(44)50-38(36-49-51(45,46)48-34-37(42)33-41)35-47-39(43)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h13,15,37-38,41-42H,3-12,14,16-36H2,1-2H3,(H,45,46)/b15-13-/t37-,38+/m0/s1
InChIKey 
ADYWCMPUNIVOEA-GPJPVTGXSA-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
PF00115' 'PF00510' 'PF02046' 'PF02285' 'PF02297' 'PF02936' 'PF05392

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)