Ligand profile

4YP

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

Bound to: KP13_03279 — Succinate dehydrogenase flavoprotein subunit

Via homolog PDB 5c2t UniProt Q33862 Formula C₁₈H₂₅NO₃
Mol. weight 303.40 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
4YP
PDB
5c2t
UniProt (similar protein)
Q33862
Target protein
KP13_03279

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 303.40 Da
LogP (Crippen) 3.35
H-bond donors 1
H-bond acceptors 4
TPSA 69.39 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 0.44
Formula C₁₈H₂₅NO₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 69.4
  • −1 ≤ LogP ≤ 5 3.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 303.4
  • LogP ≤ 5 3.35
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 69.4
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(C(=O)C(=C(C1=O)N)OC)C/C=C(\C)/CCC=C(C)C
InChI 
InChI=1S/C18H25NO3/c1-11(2)7-6-8-12(3)9-10-14-13(4)16(20)15(19)18(22-5)17(14)21/h7,9H,6,8,10,19H2,1-5H3/b12-9+
InChIKey 
WWFOMDYINFXROF-FMIVXFBMSA-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' 'PF05328' 'PF13534

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_03279.

PDB 40

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)