Ligand profile

1YY

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

Bound to: KP13_00117 — N-acetylmuramic acid 6-phosphate etherase

Via homolog PDB 4ly9 UniProt Q14397 Formula C₂₃H₃₀F₃N₃O₄S₂
Mol. weight 533.64 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
1YY
PDB
4ly9
UniProt (similar protein)
Q14397
Target protein
KP13_00117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 533.64 Da
LogP (Crippen) 3.12
H-bond donors 1
H-bond acceptors 7
TPSA 73.32 Ų
Rotatable bonds 6
Aromatic rings 2 / 4
Heavy atoms 35
Fraction sp³ C 0.57
Formula C₂₃H₃₀F₃N₃O₄S₂

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 73.3
  • −1 ≤ LogP ≤ 5 3.12
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 533.6
  • LogP ≤ 5 3.12
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 73.3
PAINS Alert

Matches PAINS filter: anil_di_alk_D(198). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1COCCN1C[C@H]2CN(CCN2c3ccc(cc3)[C@](C)(C(F)(F)F)O)S(=O)(=O)c4cccs4
InChI 
InChI=1S/C23H30F3N3O4S2/c1-17-16-33-12-11-27(17)14-20-15-28(35(31,32)21-4-3-13-34-21)9-10-29(20)19-7-5-18(6-8-19)22(2,30)23(24,25)26/h3-8,13,17,20,30H,9-12,14-16H2,1-2H3/t17-,20-,22+/m0/s1
InChIKey 
OJTJLEFGCNYTBQ-RBDMOPTHSA-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
PF20741' 'PF22645

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_00117.

PDB 16

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

Ligand PDB entry

ChEMBL 60

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)