Ligand profile

4YB

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

Bound to: VK055_4857 — O-succinylbenzoate-CoA ligase

Via homolog PDB 5c5h UniProt P37353 Formula C₂₁H₂₂N₆O₁₀S
Mol. weight 550.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4YB
PDB
5c5h
UniProt (similar protein)
P37353
Target protein
VK055_4857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 550.51 Da
LogP (Crippen) -1.23
H-bond donors 5
H-bond acceptors 14
TPSA 246.15 Ų
Rotatable bonds 10
Aromatic rings 3 / 4
Heavy atoms 38
Fraction sp³ C 0.33
Formula C₂₁H₂₂N₆O₁₀S

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 246.1
  • −1 ≤ LogP ≤ 5 -1.23
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 550.5
  • LogP ≤ 5 -1.23
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 246.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)C(=O)CCC(=O)NS(=O)(=O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)C(=O)O
InChI 
InChI=1S/C21H22N6O10S/c22-18-15-19(24-8-23-18)27(9-25-15)20-17(31)16(30)13(37-20)7-36-38(34,35)26-14(29)6-5-12(28)10-3-1-2-4-11(10)21(32)33/h1-4,8-9,13,16-17,20,30-31H,5-7H2,(H,26,29)(H,32,33)(H2,22,23,24)/t13-,16-,17-,20-/m1/s1
InChIKey 
JRKRGBFWNBVHHH-AEVYOOLXSA-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
PF00501' 'PF13193

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_4857.

PDB 11

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)