Ligand profile

C65

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 5g3w UniProt Q70I53 Formula C₁₅H₁₃N₃O₂
Mol. weight 267.29 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
C65
PDB
5g3w
UniProt (similar protein)
Q70I53
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.29 Da
LogP (Crippen) 3.62
H-bond donors 2
H-bond acceptors 4
TPSA 74.05 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 20
Fraction sp³ C 0.00
Formula C₁₅H₁₃N₃O₂

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 74.0
  • −1 ≤ LogP ≤ 5 3.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.3
  • LogP ≤ 5 3.62
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 74.0
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)/N=N/c2ccc(cc2)/C=C/C(=O)NO
InChI 
InChI=1S/C15H13N3O2/c19-15(18-20)11-8-12-6-9-14(10-7-12)17-16-13-4-2-1-3-5-13/h1-11,20H,(H,18,19)/b11-8+,17-16+
InChIKey 
FBLBOLZQIKQUIK-USZUYCLASA-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)