Ligand profile

01A

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

Bound to: VK055_4857 — O-succinylbenzoate-CoA ligase

Via homolog PDB 3cw9 UniProt Q8GN86 Formula C₂₉H₄₁ClN₇O₁₇P₃S
Mol. weight 920.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
01A
PDB
3cw9
UniProt (similar protein)
Q8GN86
Target protein
VK055_4857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 920.12 Da
LogP (Crippen) 0.67
H-bond donors 9
H-bond acceptors 19
TPSA 363.63 Ų
Rotatable bonds 22
Aromatic rings 3 / 4
Heavy atoms 58
Fraction sp³ C 0.52
Formula C₂₉H₄₁ClN₇O₁₇P₃S

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 363.6
  • −1 ≤ LogP ≤ 5 0.67
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 920.1
  • LogP ≤ 5 0.67
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 363.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSCC(=O)c4ccc(cc4)Cl)O
InChI 
InChI=1S/C29H41ClN7O17P3S/c1-29(2,24(41)27(42)33-8-7-20(39)32-9-10-58-12-18(38)16-3-5-17(30)6-4-16)13-51-57(48,49)54-56(46,47)50-11-19-23(53-55(43,44)45)22(40)28(52-19)37-15-36-21-25(31)34-14-35-26(21)37/h3-6,14-15,19,22-24,28,40-41H,7-13H2,1-2H3,(H,32,39)(H,33,42)(H,46,47)(H,48,49)(H2,31,34,35)(H2,43,44,45)/t19-,22-,23-,24+,28-/m1/s1
InChIKey 
JKZHFXZXNBMAGG-VXAHOBLNSA-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)