Ligand profile

ZINC16051958

Virtual-screening candidate from ZINC.

Bound to: VK055_3880 — octaprenyl-diphosphate synthase

Via homolog UniProt P0AD57 Formula C₂₀H₁₈O₈P₂
Tanimoto 1.00
Mol. weight 448.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC16051958
UniProt (similar protein)
P0AD57
Tanimoto
1.000
Target protein
VK055_3880

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 448.30 Da
LogP (Crippen) 3.80
H-bond donors 5
H-bond acceptors 4
TPSA 148.43 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 30
Fraction sp³ C 0.10
Formula C₂₀H₁₈O₈P₂

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 148.4
  • −1 ≤ LogP ≤ 5 3.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 448.3
  • LogP ≤ 5 3.80
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 148.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=P(O)(O)C(O)(Cc1cccc(-c2cccc3c2oc2ccccc23)c1)P(=O)(O)O
InChI 
InChI=1S/C20H18O8P2/c21-20(29(22,23)24,30(25,26)27)12-13-5-3-6-14(11-13)15-8-4-9-17-16-7-1-2-10-18(16)28-19(15)17/h1-11,21H,12H2,(H2,22,23,24)(H2,25,26,27)
InChIKey 
BYVXAUZOTGITQZ-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
B29
Homolog
P0AD57

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 3

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)