Ligand profile

0VD

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

Bound to: VK055_5044 — hisD

Via homolog PDB 4g09 UniProt Q8G2R2 Formula C₂₀H₂₁N₃O₂
Mol. weight 335.41 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0VD
PDB
4g09
UniProt (similar protein)
Q8G2R2
Target protein
VK055_5044

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.41 Da
LogP (Crippen) 2.67
H-bond donors 2
H-bond acceptors 4
TPSA 81.00 Ų
Rotatable bonds 8
Aromatic rings 3 / 3
Heavy atoms 25
Fraction sp³ C 0.20
Formula C₂₀H₂₁N₃O₂

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 81.0
  • −1 ≤ LogP ≤ 5 2.67
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.4
  • LogP ≤ 5 2.67
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 81.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)COc2ccc(cc2)CC(=O)[C@H](Cc3c[nH]cn3)N
InChI 
InChI=1S/C20H21N3O2/c21-19(11-17-12-22-14-23-17)20(24)10-15-6-8-18(9-7-15)25-13-16-4-2-1-3-5-16/h1-9,12,14,19H,10-11,13,21H2,(H,22,23)/t19-/m0/s1
InChIKey 
JPAWSYOZOLVNBT-IBGZPJMESA-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
PF00815

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_5044.

PDB 2

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

Ligand PDB entry

ChEMBL 28

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)