Ligand profile

4CA

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

Bound to: VK055_0301 — proofreading thioesterase in enterobactin biosynthesis

Via homolog PDB 1q4u UniProt Q04416 Formula C₂₈H₄₂N₇O₁₇P₃S
Mol. weight 873.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4CA
PDB
1q4u
UniProt (similar protein)
Q04416
Target protein
VK055_0301

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 873.67 Da
LogP (Crippen) 0.04
H-bond donors 10
H-bond acceptors 19
TPSA 366.79 Ų
Rotatable bonds 21
Aromatic rings 3 / 4
Heavy atoms 56
Fraction sp³ C 0.54
Formula C₂₈H₄₂N₇O₁₇P₃S

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 366.8
  • −1 ≤ LogP ≤ 5 0.04
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 873.7
  • LogP ≤ 5 0.04
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 21
  • TPSA ≤ 140 Ų 366.8
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)NCCSCc4ccc(cc4)O)O
InChI 
InChI=1S/C28H42N7O17P3S/c1-28(2,23(39)26(40)31-8-7-19(37)30-9-10-56-12-16-3-5-17(36)6-4-16)13-49-55(46,47)52-54(44,45)48-11-18-22(51-53(41,42)43)21(38)27(50-18)35-15-34-20-24(29)32-14-33-25(20)35/h3-6,14-15,18,21-23,27,36,38-39H,7-13H2,1-2H3,(H,30,37)(H,31,40)(H,44,45)(H,46,47)(H2,29,32,33)(H2,41,42,43)/t18-,21-,22-,23+,27-/m1/s1
InChIKey 
FZQUTWRNQJPTSH-SXQYHYLKSA-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
PF03061

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_0301.

PDB 8

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)