Ligand profile

JRK

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

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

Via homolog PDB 6r3n UniProt A2QHE5 Formula C₂₆H₃₃N₄O₁₁P
Mol. weight 608.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JRK
PDB
6r3n
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 608.54 Da
LogP (Crippen) -0.03
H-bond donors 7
H-bond acceptors 10
TPSA 229.76 Ų
Rotatable bonds 8
Aromatic rings 1 / 5
Heavy atoms 42
Fraction sp³ C 0.54
Formula C₂₆H₃₃N₄O₁₁P

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 229.8
  • −1 ≤ LogP ≤ 5 -0.03
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 608.5
  • LogP ≤ 5 -0.03
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 229.8
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(=C4C(=O)O)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/C26H33N4O11P/c1-10-6-13-19-18(11(10)2)25(4,5)7-14-17(21(34)35)12(3)26(30(14)19)22(27-24(37)28-23(26)36)29(13)8-15(31)20(33)16(32)9-41-42(38,39)40/h6,14-16,20,31-33H,7-9H2,1-5H3,(H,34,35)(H,28,36,37)(H2,38,39,40)/t14-,15-,16+,20-,26-/m0/s1
InChIKey 
YDFPPSZXINEINN-HHMFRQPQSA-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)