Ligand profile

JEF

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

Bound to: VK055_4139 — pepP

Via homolog PDB 6a9t UniProt P40051 Formula C₃₀H₆₃NO₁₀
Mol. weight 597.83 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JEF
PDB
6a9t
UniProt (similar protein)
P40051
Target protein
VK055_4139

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 597.83 Da
LogP (Crippen) 3.24
H-bond donors 1
H-bond acceptors 11
TPSA 118.32 Ų
Rotatable bonds 29
Aromatic rings 0 / 0
Heavy atoms 41
Fraction sp³ C 1.00
Formula C₃₀H₆₃NO₁₀

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 118.3
  • −1 ≤ LogP ≤ 5 3.24
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 597.8
  • LogP ≤ 5 3.24
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 29
  • TPSA ≤ 140 Ų 118.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](COC[C@@H](C)OC[C@@H](C)OC[C@H](C)OC[C@H](C)OCC(C)OC[C@@H](C)OC[C@@H](C)OC[C@H](C)OCCOC)N
InChI 
InChI=1S/C30H63NO10/c1-22(31)13-33-14-23(2)35-16-25(4)37-18-27(6)39-20-29(8)41-21-30(9)40-19-28(7)38-17-26(5)36-15-24(3)34-12-11-32-10/h22-30H,11-21,31H2,1-10H3/t22-,23+,24-,25+,26+,27-,28+,29-,30?/m0/s1
InChIKey 
ICCXIDTYQFYPNV-YWCYKIEYSA-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
PF00557

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_4139.

PDB 4

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)