Ligand profile

5PL

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

Bound to: KP13_20485 — Cytochrome o ubiquinol oxidase subunit 3

Via homolog PDB 2yev UniProt P98005 Formula C₆₇H₁₂₉N₂O₁₅P
Mol. weight 1233.74 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5PL
PDB
2yev
UniProt (similar protein)
P98005
Target protein
KP13_20485

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1233.74 Da
LogP (Crippen) 15.13
H-bond donors 6
H-bond acceptors 14
TPSA 245.71 Ų
Rotatable bonds 60
Aromatic rings 0 / 1
Heavy atoms 85
Fraction sp³ C 0.94
Formula C₆₇H₁₂₉N₂O₁₅P

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 245.7
  • −1 ≤ LogP ≤ 5 15.13
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 1233.7
  • LogP ≤ 5 15.13
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 60
  • TPSA ≤ 140 Ų 245.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCCCNC(=O)[C@@H](CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)NC(=O)C)OP(=O)(O)OCC(COC(=O)CCCCCCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCC(C)C
InChI 
InChI=1S/C67H129N2O15P/c1-7-8-9-10-11-12-13-14-15-16-17-18-25-30-35-40-45-50-68-66(76)60(54-80-67-63(69-57(6)71)65(75)64(74)59(51-70)83-67)84-85(77,78)81-53-58(82-62(73)49-44-39-34-29-24-20-22-27-32-37-42-47-56(4)5)52-79-61(72)48-43-38-33-28-23-19-21-26-31-36-41-46-55(2)3/h55-56,58-60,63-65,67,70,74-75H,7-54H2,1-6H3,(H,68,76)(H,69,71)(H,77,78)/t58?,59-,60-,63-,64-,65-,67+/m1/s1
InChIKey 
LEQHPGOQHCQGAI-RIOFPHLUSA-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
PF00115' 'PF00510

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)