Ligand profile

EB4

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

Bound to: KP13_05375 — Ferric enterobactin receptor

Via homolog PDB 6i2j UniProt Q05098 Formula C₃₀H₂₇N₃O₁₅
Mol. weight 669.55 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
EB4
PDB
6i2j
UniProt (similar protein)
Q05098
Target protein
KP13_05375

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 669.55 Da
LogP (Crippen) -0.74
H-bond donors 9
H-bond acceptors 15
TPSA 287.58 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 48
Fraction sp³ C 0.20
Formula C₃₀H₂₇N₃O₁₅

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 287.6
  • −1 ≤ LogP ≤ 5 -0.74
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 669.6
  • LogP ≤ 5 -0.74
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 287.6
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(c(c1)O)O)C(=O)N[C@H]2COC(=O)[C@H](COC(=O)[C@H](COC2=O)NC(=O)c3cccc(c3O)O)NC(=O)c4cccc(c4O)O
InChI 
InChI=1S/C30H27N3O15/c34-19-7-1-4-13(22(19)37)25(40)31-16-10-46-29(44)18(33-27(42)15-6-3-9-21(36)24(15)39)12-48-30(45)17(11-47-28(16)43)32-26(41)14-5-2-8-20(35)23(14)38/h1-9,16-18,34-39H,10-12H2,(H,31,40)(H,32,41)(H,33,42)/t16-,17-,18-/m0/s1
InChIKey 
SERBHKJMVBATSJ-BZSNNMDCSA-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
PF00593

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_05375.

PDB 12

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)