Ligand profile

9RB

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 5li3 UniProt Q9HXM1 Formula C₁₅H₁₇N₅O₂
Mol. weight 299.33 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
9RB
PDB
5li3
UniProt (similar protein)
Q9HXM1
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 299.33 Da
LogP (Crippen) 2.97
H-bond donors 2
H-bond acceptors 6
TPSA 91.87 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 22
Fraction sp³ C 0.20
Formula C₁₅H₁₇N₅O₂

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 91.9
  • −1 ≤ LogP ≤ 5 2.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 299.3
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 91.9
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 
Cc1c(c(n(n1)C)C)/N=N/c2ccc(cc2)/C=C/C(=O)NO
InChI 
InChI=1S/C15H17N5O2/c1-10-15(11(2)20(3)18-10)17-16-13-7-4-12(5-8-13)6-9-14(21)19-22/h4-9,22H,1-3H3,(H,19,21)/b9-6+,17-16+
InChIKey 
GGZOJTXQALEQJU-OUWLFTCQSA-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)