Ligand profile

FBJ

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6css UniProt F8W4B7 Formula C₆H₉NO₂
Mol. weight 127.14 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FBJ
PDB
6css
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 127.14 Da
LogP (Crippen) 0.60
H-bond donors 2
H-bond acceptors 2
TPSA 49.33 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 9
Fraction sp³ C 0.50
Formula C₆H₉NO₂

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 0.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 127.1
  • LogP ≤ 5 0.60
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 49.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CC=C(C1)C(=O)NO
InChI 
InChI=1S/C6H9NO2/c8-6(7-9)5-3-1-2-4-5/h3,9H,1-2,4H2,(H,7,8)
InChIKey 
RYYGSXXWQSXKRP-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)