Ligand profile

HJX

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

Bound to: VK055_3880 — octaprenyl-diphosphate synthase

Via homolog PDB 5ze6 UniProt P0AD57 Formula C₂₁H₃₄O₄
Mol. weight 350.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HJX
PDB
5ze6
UniProt (similar protein)
P0AD57
Target protein
VK055_3880

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 350.50 Da
LogP (Crippen) 6.17
H-bond donors 2
H-bond acceptors 3
TPSA 66.76 Ų
Rotatable bonds 15
Aromatic rings 1 / 1
Heavy atoms 25
Fraction sp³ C 0.67
Formula C₂₁H₃₄O₄

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 66.8
  • −1 ≤ LogP ≤ 5 6.17
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 350.5
  • LogP ≤ 5 6.17
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 66.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCOc1cccc(c1C(=O)O)O
InChI 
InChI=1S/C21H34O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-17-25-19-16-14-15-18(22)20(19)21(23)24/h14-16,22H,2-13,17H2,1H3,(H,23,24)
InChIKey 
COUQHIRIFUVLDU-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
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 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)