Ligand profile

3ZV

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 4xdh UniProt P16083 Formula C₁₆H₁₃NO₃
Mol. weight 267.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3ZV
PDB
4xdh
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.28 Da
LogP (Crippen) 3.02
H-bond donors 0
H-bond acceptors 4
TPSA 47.89 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.12
Formula C₁₆H₁₃NO₃

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 47.9
  • −1 ≤ LogP ≤ 5 3.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.3
  • LogP ≤ 5 3.02
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 47.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1)C2=Nc3ccc(cc3C2=O)OC
InChI 
InChI=1S/C16H13NO3/c1-19-11-5-3-10(4-6-11)15-16(18)13-9-12(20-2)7-8-14(13)17-15/h3-9H,1-2H3
InChIKey 
VCLRIWYAOAOICS-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)