Ligand profile

MCM

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 5efk UniProt F8W4B7 Formula C₁₀H₉NO₂
Mol. weight 175.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MCM
PDB
5efk
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.19 Da
LogP (Crippen) 1.68
H-bond donors 1
H-bond acceptors 3
TPSA 56.23 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 13
Fraction sp³ C 0.10
Formula C₁₀H₉NO₂

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 56.2
  • −1 ≤ LogP ≤ 5 1.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.2
  • LogP ≤ 5 1.68
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 56.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CC(=O)Oc2c1ccc(c2)N
InChI 
InChI=1S/C10H9NO2/c1-6-4-10(12)13-9-5-7(11)2-3-8(6)9/h2-5H,11H2,1H3
InChIKey 
GLNDAGDHSLMOKX-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)