Ligand profile

ZINC13519179

Virtual-screening candidate from ZINC.

Bound to: KP13_00750 — 50S ribosomal protein L4

Via homolog UniProt Q5SHN9 Formula C₉H₁₂N₂O₆
Tanimoto 0.67
Mol. weight 244.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13519179
UniProt (similar protein)
Q5SHN9
Tanimoto
0.667
Target protein
KP13_00750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 244.20 Da
LogP (Crippen) -2.78
H-bond donors 5
H-bond acceptors 6
TPSA 135.64 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.56
Formula C₉H₁₂N₂O₆

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 135.6
  • −1 ≤ LogP ≤ 5 -2.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 244.2
  • LogP ≤ 5 -2.78
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 135.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1[nH]cc([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6+,7+/m1/s1
InChIKey 
PTJWIQPHWPFNBW-JWXFUTCRSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
PSU
Homolog
Q5SHN9

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_00750.

PDB 7

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)