Ligand profile

YMZ

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

Bound to: KP13_03996 — 50S ribosomal protein L13

Via homolog PDB 5umd UniProt Q8IJZ7 Formula C₁₇H₁₆F₆N₂O
Mol. weight 378.32 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YMZ
PDB
5umd
UniProt (similar protein)
Q8IJZ7
Target protein
KP13_03996

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.32 Da
LogP (Crippen) 4.45
H-bond donors 2
H-bond acceptors 3
TPSA 45.15 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.47
Formula C₁₇H₁₆F₆N₂O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 45.2
  • −1 ≤ LogP ≤ 5 4.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 378.3
  • LogP ≤ 5 4.45
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 45.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc(nc2c(c1)C(F)(F)F)C(F)(F)F)[C@H]([C@@H]3CCCCN3)O
InChI 
InChI=1S/C17H16F6N2O/c18-16(19,20)11-5-3-4-9-10(15(26)12-6-1-2-7-24-12)8-13(17(21,22)23)25-14(9)11/h3-5,8,12,15,24,26H,1-2,6-7H2/t12-,15+/m0/s1
InChIKey 
XEEQGYMUWCZPDN-SWLSCSKDSA-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
PF00572' 'PF14374

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_03996.

PDB 4

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)