Ligand profile

3ZU

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 4xdg UniProt P16083 Formula C₁₅H₁₂N₂O₃
Mol. weight 268.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3ZU
PDB
4xdg
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 268.27 Da
LogP (Crippen) 2.10
H-bond donors 1
H-bond acceptors 4
TPSA 78.39 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.07
Formula C₁₅H₁₂N₂O₃

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 78.4
  • −1 ≤ LogP ≤ 5 2.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 268.3
  • LogP ≤ 5 2.10
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c(c1)C(=O)C(=[N+]2[O-])c3ccc(cc3)N
InChI 
InChI=1S/C15H12N2O3/c1-20-11-6-7-13-12(8-11)15(18)14(17(13)19)9-2-4-10(16)5-3-9/h2-8H,16H2,1H3
InChIKey 
HTBDGBPUYWVYCA-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)