Ligand profile

372

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 4gr9 UniProt P16083 Formula C₁₃H₁₃N₃O₂
Mol. weight 243.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
372
PDB
4gr9
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.27 Da
LogP (Crippen) 1.62
H-bond donors 1
H-bond acceptors 3
TPSA 73.20 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.31
Formula C₁₃H₁₃N₃O₂

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 73.2
  • −1 ≤ LogP ≤ 5 1.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 243.3
  • LogP ≤ 5 1.62
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 73.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)Nc1ccc2c(c1)C(C(=O)N2C)CC#N
InChI 
InChI=1S/C13H13N3O2/c1-8(17)15-9-3-4-12-11(7-9)10(5-6-14)13(18)16(12)2/h3-4,7,10H,5H2,1-2H3,(H,15,17)
InChIKey 
PFJVUECMVVMLTI-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)