Ligand profile

3YP

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 1zz3 UniProt Q70I53 Formula C₈H₁₅NO₂
Mol. weight 157.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3YP
PDB
1zz3
UniProt (similar protein)
Q70I53
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 157.21 Da
LogP (Crippen) 1.46
H-bond donors 2
H-bond acceptors 2
TPSA 49.33 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 11
Fraction sp³ C 0.88
Formula C₈H₁₅NO₂

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 49.3
  • −1 ≤ LogP ≤ 5 1.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 157.2
  • LogP ≤ 5 1.46
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 49.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(C1)CCC(=O)NO
InChI 
InChI=1S/C8H15NO2/c10-8(9-11)6-5-7-3-1-2-4-7/h7,11H,1-6H2,(H,9,10)
InChIKey 
PCDWXHSMVLWAMG-UHFFFAOYSA-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
PF00850

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_03495.

PDB 45

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 55

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)