Ligand profile

CDN

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

Bound to: KP13_31481 — Fumarate reductase flavoprotein subunit

Via homolog PDB 1nek UniProt P0AC41 Formula C₅₈H₁₂₀O₁₇P₂
Mol. weight 1151.53 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CDN
PDB
1nek
UniProt (similar protein)
P0AC41
Target protein
KP13_31481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1151.53 Da
LogP (Crippen) 14.77
H-bond donors 7
H-bond acceptors 15
TPSA 249.59 Ų
Rotatable bonds 63
Aromatic rings 0 / 0
Heavy atoms 77
Fraction sp³ C 1.00
Formula C₅₈H₁₂₀O₁₇P₂

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 249.6
  • −1 ≤ LogP ≤ 5 14.77
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 1151.5
  • LogP ≤ 5 14.77
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 63
  • TPSA ≤ 140 Ų 249.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCC(O)O[C@H](COC(CCCCC)O)CO[P@@](=O)(O)OC[C@@H](CO[P@@](=O)(O)OC[C@@H](COC(CCCCCCCCCCCC)O)O[C@@H](CCCCCCCCCCCCCC)O)O
InChI 
InChI=1S/C58H120O17P2/c1-5-9-13-16-19-22-25-27-30-33-36-40-44-57(62)74-53(48-68-55(60)42-38-12-8-4)50-72-76(64,65)70-46-52(59)47-71-77(66,67)73-51-54(49-69-56(61)43-39-35-32-29-24-21-18-15-11-7-3)75-58(63)45-41-37-34-31-28-26-23-20-17-14-10-6-2/h52-63H,5-51H2,1-4H3,(H,64,65)(H,66,67)/t52-,53+,54+,55?,56?,57?,58-/m0/s1
InChIKey 
GKRASOJOCMJQMF-DUXRJKJQSA-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
PF01127

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_31481.

PDB 35

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)