Ligand profile

JSH

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

Bound to: VK055_3138 — 3-octaprenyl-4-hydroxybenzoate decarboxylase

Via homolog PDB 6r3l UniProt A2QHE5 Formula C₃₀H₃₇N₄O₉P
Mol. weight 628.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JSH
PDB
6r3l
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 628.62 Da
LogP (Crippen) 1.75
H-bond donors 6
H-bond acceptors 9
TPSA 192.46 Ų
Rotatable bonds 8
Aromatic rings 2 / 6
Heavy atoms 44
Fraction sp³ C 0.50
Formula C₃₀H₃₇N₄O₉P

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 192.5
  • −1 ≤ LogP ≤ 5 1.75
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 628.6
  • LogP ≤ 5 1.75
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 192.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5([C@@H](C4)c6ccccc6)C(=O)NC(=O)N=C5N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)(C)C
InChI 
InChI=1S/C30H37N4O9P/c1-15-10-20-24-23(16(15)2)29(3,4)12-18-11-19(17-8-6-5-7-9-17)30(34(18)24)26(31-28(39)32-27(30)38)33(20)13-21(35)25(37)22(36)14-43-44(40,41)42/h5-10,18-19,21-22,25,35-37H,11-14H2,1-4H3,(H,32,38,39)(H2,40,41,42)/t18-,19+,21+,22-,25+,30+/m1/s1
InChIKey 
WCKFFLZBWSLRDK-BEFVXGCNSA-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
PF01977' 'PF20696

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_3138.

PDB 21

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)