Ligand profile

9Y0

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

Bound to: KP13_20485 — Cytochrome o ubiquinol oxidase subunit 3

Via homolog PDB 6adq UniProt A0R049 Formula C₃₉H₇₆NO₈P
Mol. weight 718.01 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9Y0
PDB
6adq
UniProt (similar protein)
A0R049
Target protein
KP13_20485

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 718.01 Da
LogP (Crippen) 11.05
H-bond donors 2
H-bond acceptors 8
TPSA 134.38 Ų
Rotatable bonds 38
Aromatic rings 0 / 0
Heavy atoms 49
Fraction sp³ C 0.90
Formula C₃₉H₇₆NO₈P

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 134.4
  • −1 ≤ LogP ≤ 5 11.05
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 718.0
  • LogP ≤ 5 11.05
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 38
  • TPSA ≤ 140 Ų 134.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC/C=C\CCCCCCCC)COP(=O)(O)OCCN
InChI 
InChI=1S/C39H76NO8P/c1-3-5-7-9-11-13-15-17-18-20-21-23-25-27-29-31-38(41)45-35-37(36-47-49(43,44)46-34-33-40)48-39(42)32-30-28-26-24-22-19-16-14-12-10-8-6-4-2/h17-18,37H,3-16,19-36,40H2,1-2H3,(H,43,44)/b18-17-/t37-/m1/s1
InChIKey 
DVXMEPWDARXHCX-OTMQOFQLSA-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
PF00510' 'PF13631

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)