Ligand profile

HJN

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

Bound to: VK055_4167 — 3-octaprenyl-4-hydroxybenzoate decarboxylase together with UbiG

Via homolog PDB 6qlv UniProt A0A072ZCW8 Formula C₂₇H₃₉N₄O₉P
Mol. weight 594.60 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HJN
PDB
6qlv
UniProt (similar protein)
A0A072ZCW8
Target protein
VK055_4167

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 594.60 Da
LogP (Crippen) 2.15
H-bond donors 7
H-bond acceptors 9
TPSA 199.65 Ų
Rotatable bonds 12
Aromatic rings 2 / 3
Heavy atoms 41
Fraction sp³ C 0.48
Formula C₂₇H₃₉N₄O₉P

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 199.6
  • −1 ≤ LogP ≤ 5 2.15
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 594.6
  • LogP ≤ 5 2.15
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 199.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1C)N(C3=C(N2C/C=C(/C)\CCC=C(C)C)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
InChI 
InChI=1S/C27H39N4O9P/c1-15(2)7-6-8-16(3)9-10-30-19-11-17(4)18(5)12-20(19)31(25-23(30)26(35)29-27(36)28-25)13-21(32)24(34)22(33)14-40-41(37,38)39/h7,9,11-12,21-22,24,32-34H,6,8,10,13-14H2,1-5H3,(H2,37,38,39)(H2,28,29,35,36)/b16-9-/t21-,22+,24-/m0/s1
InChIKey 
NUMSCVAFXSDOGX-QKMBGELKSA-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
PF02441

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_4167.

PDB 7

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

Ligand PDB entry

ZINC 25

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

Compound Similarity (Tanimoto)