Ligand profile

R5G

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6vnr UniProt F8W4B7 Formula C₁₇H₁₅N₃O₄
Mol. weight 325.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R5G
PDB
6vnr
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 325.32 Da
LogP (Crippen) 1.93
H-bond donors 4
H-bond acceptors 5
TPSA 103.59 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.06
Formula C₁₇H₁₅N₃O₄

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 103.6
  • −1 ≤ LogP ≤ 5 1.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 325.3
  • LogP ≤ 5 1.93
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 103.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1Cn2ccc3c2cc(cc3)C(=O)NO)C(=O)NO
InChI 
InChI=1S/C17H15N3O4/c21-16(18-23)13-3-1-11(2-4-13)10-20-8-7-12-5-6-14(9-15(12)20)17(22)19-24/h1-9,23-24H,10H2,(H,18,21)(H,19,22)
InChIKey 
IRJZGNPPEWBPKI-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)