Ligand profile

PEE

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

Bound to: KP13_04075 — Cytochrome oxidase bd-II, subunit 1

Via homolog PDB 6rx4 UniProt P0ABJ9 Formula C₄₁H₇₈NO₈P
Mol. weight 744.05 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PEE
PDB
6rx4
UniProt (similar protein)
P0ABJ9
Target protein
KP13_04075

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 744.05 Da
LogP (Crippen) 11.61
H-bond donors 2
H-bond acceptors 8
TPSA 134.38 Ų
Rotatable bonds 39
Aromatic rings 0 / 0
Heavy atoms 51
Fraction sp³ C 0.85
Formula C₄₁H₇₈NO₈P

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 11.61
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 744.0
  • LogP ≤ 5 11.61
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 39
  • TPSA ≤ 140 Ų 134.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC(=O)CCCCCCC/C=C\CCCCCCCC
InChI 
InChI=1S/C41H78NO8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(43)47-37-39(38-49-51(45,46)48-36-35-42)50-41(44)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h17-20,39H,3-16,21-38,42H2,1-2H3,(H,45,46)/b19-17-,20-18-/t39-/m1/s1
InChIKey 
MWRBNPKJOOWZPW-NYVOMTAGSA-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
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 KP13_04075.

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)