Ligand profile

JQK

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

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

Via homolog PDB 6r3f UniProt A2QHE5 Formula C₃₀H₃₉N₄O₉P
Mol. weight 630.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JQK
PDB
6r3f
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 630.64 Da
LogP (Crippen) 2.56
H-bond donors 7
H-bond acceptors 10
TPSA 199.91 Ų
Rotatable bonds 10
Aromatic rings 3 / 5
Heavy atoms 44
Fraction sp³ C 0.47
Formula C₃₀H₃₉N₄O₉P

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 199.9
  • −1 ≤ LogP ≤ 5 2.56
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 630.6
  • LogP ≤ 5 2.56
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 199.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)N=C(NC4=O)O)CCc5ccccc5)(C)C
InChI 
InChI=1S/C30H39N4O9P/c1-16-12-20-24-23(17(16)2)30(3,4)13-19(11-10-18-8-6-5-7-9-18)34(24)25-27(31-29(39)32-28(25)38)33(20)14-21(35)26(37)22(36)15-43-44(40,41)42/h5-9,12,19,21-22,26,35-37H,10-11,13-15H2,1-4H3,(H2,40,41,42)(H2,31,32,38,39)/t19-,21+,22-,26+/m1/s1
InChIKey 
XFXQWHPAGKZXHS-MRESPNAKSA-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)