Ligand profile

PLX

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

Bound to: KP13_00989 — NADH-quinone oxidoreductase subunit F

Via homolog PDB 5gup UniProt A0A4X1SZP7 Formula C₄₂H₈₉NO₈P⁺
Mol. weight 767.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PLX
PDB
5gup
UniProt (similar protein)
A0A4X1SZP7
Target protein
KP13_00989

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 767.15 Da
LogP (Crippen) 11.61
H-bond donors 3
H-bond acceptors 7
TPSA 114.68 Ų
Rotatable bonds 42
Aromatic rings 0 / 0
Heavy atoms 52
Fraction sp³ C 1.00
Formula C₄₂H₈₉NO₈P⁺

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 114.7
  • −1 ≤ LogP ≤ 5 11.61
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 767.1
  • LogP ≤ 5 11.61
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 42
  • TPSA ≤ 140 Ų 114.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCCCCCCCCCCCC)O)CO[P@](=O)(O)OCC[N+](C)(C)C
InChI 
InChI=1S/C42H88NO8P/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/h40-42,44-45H,6-39H2,1-5H3/p+1/t40-,41+,42+/m1/s1
InChIKey 
YVNJQRQLQPWVSQ-IWSHAHEXSA-O

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
PF00033' 'PF00146' 'PF00346' 'PF00361' 'PF02466' 'PF02921' 'PF05365' 'PF06444

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_00989.

PDB 19

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)