Ligand profile

M42

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 3nhu UniProt P16083 Formula C₁₁H₉NO₃
Mol. weight 203.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M42
PDB
3nhu
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 203.20 Da
LogP (Crippen) 1.57
H-bond donors 1
H-bond acceptors 3
TPSA 51.32 Ų
Rotatable bonds 0
Aromatic rings 2 / 3
Heavy atoms 15
Fraction sp³ C 0.18
Formula C₁₁H₉NO₃

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 51.3
  • −1 ≤ LogP ≤ 5 1.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 203.2
  • LogP ≤ 5 1.57
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 51.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CC(=O)Nc2c1ccc3c2OCO3
InChI 
InChI=1S/C11H9NO3/c1-6-4-9(13)12-10-7(6)2-3-8-11(10)15-5-14-8/h2-4H,5H2,1H3,(H,12,13)
InChIKey 
XCKXJOHJSMHNFE-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
PF02525

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2684.

PDB 59

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

Ligand PDB entry

ChEMBL 100

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)