Ligand profile

ZE8

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

Bound to: KP13_03756 — Nucleoside permease nupC

Via homolog PDB 4pd7 UniProt Q9KPL5 Formula C₉H₁₂N₂O₅
Mol. weight 228.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZE8
PDB
4pd7
UniProt (similar protein)
Q9KPL5
Target protein
KP13_03756

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 228.20 Da
LogP (Crippen) -2.15
H-bond donors 3
H-bond acceptors 7
TPSA 104.81 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.56
Formula C₉H₁₂N₂O₅

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 104.8
  • −1 ≤ LogP ≤ 5 -2.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 228.2
  • LogP ≤ 5 -2.15
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 104.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
InChI 
InChI=1S/C9H12N2O5/c12-4-5-6(13)7(14)8(16-5)11-3-1-2-10-9(11)15/h1-3,5-8,12-14H,4H2/t5-,6-,7-,8-/m1/s1
InChIKey 
RPQZTTQVRYEKCR-WCTZXXKLSA-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
PF07662' 'PF07670

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_03756.

PDB 9

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)