Ligand profile

9YF

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 C₄₄H₈₅O₁₃P
Mol. weight 853.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9YF
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 853.13 Da
LogP (Crippen) 8.75
H-bond donors 6
H-bond acceptors 12
TPSA 209.51 Ų
Rotatable bonds 38
Aromatic rings 0 / 1
Heavy atoms 58
Fraction sp³ C 0.95
Formula C₄₄H₈₅O₁₃P

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 209.5
  • −1 ≤ LogP ≤ 5 8.75
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 853.1
  • LogP ≤ 5 8.75
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 38
  • TPSA ≤ 140 Ų 209.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC[C@@H](C)CCCCCCCCC)COP(=O)(O)OC1[C@@H]([C@@H](C([C@H]([C@@H]1O)O)O)O)O
InChI 
InChI=1S/C44H85O13P/c1-4-6-8-10-12-13-14-15-16-17-19-23-28-32-38(46)56-36(34-55-58(52,53)57-44-42(50)40(48)39(47)41(49)43(44)51)33-54-37(45)31-27-24-20-22-26-30-35(3)29-25-21-18-11-9-7-5-2/h35-36,39-44,47-51H,4-34H2,1-3H3,(H,52,53)/t35-,36+,39?,40+,41+,42-,43+,44?/m0/s1
InChIKey 
GRDWPDVMAXODDM-GOLNVTOWSA-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
PF12270' 'PF13442' '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)