Ligand profile

MBD

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

Bound to: KP13_02713 — Glyoxalase/Bleomycin resistance protein/Dioxygenase domain-containing protein

Via homolog PDB 1knf UniProt P47228 Formula C₇H₈O₂
Mol. weight 124.14 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
MBD
PDB
1knf
UniProt (similar protein)
P47228
Target protein
KP13_02713

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 124.14 Da
LogP (Crippen) 1.41
H-bond donors 2
H-bond acceptors 2
TPSA 40.46 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.14
Formula C₇H₈O₂

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 40.5
  • −1 ≤ LogP ≤ 5 1.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 124.1
  • LogP ≤ 5 1.41
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 40.5
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cccc(c1O)O
InChI 
InChI=1S/C7H8O2/c1-5-3-2-4-6(8)7(5)9/h2-4,8-9H,1H3
InChIKey 
PGSWEKYNAOWQDF-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
PF00903

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_02713.

PDB 7

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)