Ligand profile

2DE

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

Bound to: VK055_3880 — octaprenyl-diphosphate synthase

Via homolog PDB 3aqc UniProt O66129 Formula C₁₄H₂₆O₇P₂
Mol. weight 368.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2DE
PDB
3aqc
UniProt (similar protein)
O66129
Target protein
VK055_3880

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 368.30 Da
LogP (Crippen) 4.24
H-bond donors 3
H-bond acceptors 4
TPSA 113.29 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 0.57
Formula C₁₄H₂₆O₇P₂

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 113.3
  • −1 ≤ LogP ≤ 5 4.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 368.3
  • LogP ≤ 5 4.24
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 113.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=CCC/C(=C/CC/C=C/CO[P@](=O)(O)OP(=O)(O)O)/C)C
InChI 
InChI=1S/C14H26O7P2/c1-13(2)9-8-11-14(3)10-6-4-5-7-12-20-23(18,19)21-22(15,16)17/h5,7,9-10H,4,6,8,11-12H2,1-3H3,(H,18,19)(H2,15,16,17)/b7-5+,14-10+
InChIKey 
AFSHNJXUHHFZPQ-XOBXVUKQSA-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
PF00348' 'PF22538

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 7

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 50

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

Compound Similarity (Tanimoto)