Ligand profile

NGE

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

Bound to: KP13_05461 — Periplasmic murein peptide-binding protein

Via homolog PDB 5yyb UniProt Q7VL18 Formula C₁₁H₁₉NO₁₀
Mol. weight 325.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NGE
PDB
5yyb
UniProt (similar protein)
Q7VL18
Target protein
KP13_05461

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 325.27 Da
LogP (Crippen) -4.90
H-bond donors 8
H-bond acceptors 9
TPSA 197.01 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 0.82
Formula C₁₁H₁₉NO₁₀

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 197.0
  • −1 ≤ LogP ≤ 5 -4.90
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 325.3
  • LogP ≤ 5 -4.90
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 197.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)NC(=O)CO)O
InChI 
InChI=1S/C11H19NO10/c13-2-5(16)8(18)9-7(12-6(17)3-14)4(15)1-11(21,22-9)10(19)20/h4-5,7-9,13-16,18,21H,1-3H2,(H,12,17)(H,19,20)/t4-,5+,7+,8+,9+,11-/m0/s1
InChIKey 
FDJKUWYYUZCUJX-AJKRCSPLSA-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
PF00496

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_05461.

PDB 20

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)