Ligand profile

JRH

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

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

Via homolog PDB 6r3j UniProt A2QHE5 Formula C₂₅H₃₅N₄O₉P
Mol. weight 566.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JRH
PDB
6r3j
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 566.55 Da
LogP (Crippen) 0.60
H-bond donors 6
H-bond acceptors 9
TPSA 192.46 Ų
Rotatable bonds 7
Aromatic rings 1 / 5
Heavy atoms 39
Fraction sp³ C 0.64
Formula C₂₅H₃₅N₄O₉P

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 0.60
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 566.5
  • LogP ≤ 5 0.60
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • 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)C)C(=O)NC(=O)N=C5N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)(C)C
InChI 
InChI=1S/C25H35N4O9P/c1-11-6-15-19-18(13(11)3)24(4,5)8-14-7-12(2)25(29(14)19)21(26-23(34)27-22(25)33)28(15)9-16(30)20(32)17(31)10-38-39(35,36)37/h6,12,14,16-17,20,30-32H,7-10H2,1-5H3,(H,27,33,34)(H2,35,36,37)/t12-,14-,16+,17-,20+,25+/m1/s1
InChIKey 
FBBFRJDRDBTJFO-VOBMUHBHSA-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)