Ligand profile

POV

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

Bound to: VK055_0551 — bacterial Cytochrome Ubiquinol Oxidase family protein

Via homolog PDB 6rko UniProt P0ABJ9 Formula C₄₂H₈₂NO₈P
Mol. weight 760.09 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
POV
PDB
6rko
UniProt (similar protein)
P0ABJ9
Target protein
VK055_0551

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 760.09 Da
LogP (Crippen) 11.17
H-bond donors 0
H-bond acceptors 8
TPSA 111.19 Ų
Rotatable bonds 39
Aromatic rings 0 / 0
Heavy atoms 52
Fraction sp³ C 0.90
Formula C₄₂H₈₂NO₈P

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 111.2
  • −1 ≤ LogP ≤ 5 11.17
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 760.1
  • LogP ≤ 5 11.17
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 39
  • TPSA ≤ 140 Ų 111.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P@](=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCCCC/C=C\CCCCCCCC
InChI 
InChI=1S/C42H82NO8P/c1-6-8-10-12-14-16-18-20-21-23-25-27-29-31-33-35-42(45)51-40(39-50-52(46,47)49-37-36-43(3,4)5)38-48-41(44)34-32-30-28-26-24-22-19-17-15-13-11-9-7-2/h20-21,40H,6-19,22-39H2,1-5H3/b21-20-/t40-/m0/s1
InChIKey 
WTJKGGKOPKCXLL-PFDVCBLKSA-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
PF01654' 'PF02322

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_0551.

PDB 4

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)