Ligand profile

CHEMBL407221

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_3880 — octaprenyl-diphosphate synthase

Via homolog UniProt Q964Q8 Formula C₅H₁₅NO₆P₂
pchembl 6.12 ~758.6 nM
Mol. weight 247.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL407221
UniProt (similar protein)
Q964Q8
pchembl
6.120 (~758.6 nM)
Target protein
VK055_3880

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 247.12 Da
LogP (Crippen) -0.33
H-bond donors 5
H-bond acceptors 3
TPSA 127.09 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 1.00
Formula C₅H₁₅NO₆P₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 127.1
  • −1 ≤ LogP ≤ 5 -0.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 247.1
  • LogP ≤ 5 -0.33
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 127.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)NCC(P(=O)(O)O)P(=O)(O)O
InChI 
InChI=1S/C5H15NO6P2/c1-4(2)6-3-5(13(7,8)9)14(10,11)12/h4-6H,3H2,1-2H3,(H2,7,8,9)(H2,10,11,12)
InChIKey 
XUKNZUJYUAFJQJ-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
ChEMBL
Binding sites
PF00348

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_3880.

PDB 8

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

Ligand PDB entry

ChEMBL 2

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)