Ligand profile

V0D

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

Bound to: VK055_2378 — di-trans,poly-cis-decaprenylcistransferase

Via homolog PDB 7jlr UniProt O31751 Formula C₂₀H₂₃FN₄
Mol. weight 338.43 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
V0D
PDB
7jlr
UniProt (similar protein)
O31751
Target protein
VK055_2378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 338.43 Da
LogP (Crippen) 4.48
H-bond donors 0
H-bond acceptors 4
TPSA 33.43 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 25
Fraction sp³ C 0.40
Formula C₂₀H₂₃FN₄

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 33.4
  • −1 ≤ LogP ≤ 5 4.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 338.4
  • LogP ≤ 5 4.48
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 33.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1cc(n2c(n1)c(cn2)c3ccc(cc3)F)N4CCCCCC4
InChI 
InChI=1S/C20H23FN4/c1-2-17-13-19(24-11-5-3-4-6-12-24)25-20(23-17)18(14-22-25)15-7-9-16(21)10-8-15/h7-10,13-14H,2-6,11-12H2,1H3
InChIKey 
BQIPJVLJUIILIA-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
PF01255

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_2378.

PDB 3

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

Ligand PDB entry

ChEMBL 17

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)