Ligand profile

EEB

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

Bound to: KP13_01348 — UDP-N-acetylenolpyruvoylglucosamine reductase

Via homolog PDB 1mbb UniProt P08373 Formula C₂₁H₃₃N₃O₁₉P₂
Mol. weight 693.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EEB
PDB
1mbb
UniProt (similar protein)
P08373
Target protein
KP13_01348

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 693.45 Da
LogP (Crippen) -3.76
H-bond donors 9
H-bond acceptors 17
TPSA 332.16 Ų
Rotatable bonds 14
Aromatic rings 1 / 3
Heavy atoms 45
Fraction sp³ C 0.71
Formula C₂₁H₃₃N₃O₁₉P₂

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 332.2
  • −1 ≤ LogP ≤ 5 -3.76
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 693.4
  • LogP ≤ 5 -3.76
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 332.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC(C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
InChI 
InChI=1S/C21H33N3O19P2/c1-3-9(19(31)32)39-17-13(22-8(2)26)20(41-10(6-25)15(17)29)42-45(36,37)43-44(34,35)38-7-11-14(28)16(30)18(40-11)24-5-4-12(27)23-21(24)33/h4-5,9-11,13-18,20,25,28-30H,3,6-7H2,1-2H3,(H,22,26)(H,31,32)(H,34,35)(H,36,37)(H,23,27,33)/t9?,10-,11-,13-,14-,15-,16-,17-,18-,20-/m1/s1
InChIKey 
DFCARJAECCPPGB-NFOAWVKWSA-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
PF01565' 'PF02873

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_01348.

PDB 3

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 35

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)