Ligand profile

ZINC59846619

Virtual-screening candidate from ZINC.

Bound to: KP13_02425 — 30S ribosomal protein S16

Via homolog UniProt Q5SJH3 Formula C₁₂H₂₆N₄O₆
Tanimoto 0.70
Mol. weight 322.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC59846619
UniProt (similar protein)
Q5SJH3
Tanimoto
0.698
Target protein
KP13_02425

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 322.36 Da
LogP (Crippen) -5.12
H-bond donors 8
H-bond acceptors 10
TPSA 203.46 Ų
Rotatable bonds 3
Aromatic rings 0 / 2
Heavy atoms 22
Fraction sp³ C 1.00
Formula C₁₂H₂₆N₄O₆

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 203.5
  • −1 ≤ LogP ≤ 5 -5.12
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 322.4
  • LogP ≤ 5 -5.12
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 203.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@@H](N)C[C@H]2N)[C@H](N)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C12H26N4O6/c13-2-5-8(18)9(19)6(16)12(21-5)22-11-4(15)1-3(14)7(17)10(11)20/h3-12,17-20H,1-2,13-16H2/t3-,4+,5-,6+,7-,8+,9-,10-,11+,12+/m0/s1
InChIKey 
SYJXFKPQNSDJLI-QJDHDDNUSA-N

Provenance

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

Method
LigQ nearest_k
Query
NMY
Homolog
Q5SJH3

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_02425.

PDB 6

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)