Ligand profile

C09

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 5lbu UniProt P16083 Formula C₁₃H₁₄N₄O
Mol. weight 242.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C09
PDB
5lbu
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 242.28 Da
LogP (Crippen) 2.23
H-bond donors 2
H-bond acceptors 4
TPSA 76.82 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 18
Fraction sp³ C 0.23
Formula C₁₃H₁₄N₄O

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 76.8
  • −1 ≤ LogP ≤ 5 2.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 242.3
  • LogP ≤ 5 2.23
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 76.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOCc1[nH]c2c3ccccc3nc(c2n1)N
InChI 
InChI=1S/C13H14N4O/c1-2-18-7-10-16-11-8-5-3-4-6-9(8)15-13(14)12(11)17-10/h3-6H,2,7H2,1H3,(H2,14,15)(H,16,17)
InChIKey 
DEVCLHVFELRPIU-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)