Ligand profile

MG9

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

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

Via homolog PDB 4mqu UniProt Q14397 Formula C₂₁H₂₀F₆N₄O₃S
Mol. weight 522.47 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
MG9
PDB
4mqu
UniProt (similar protein)
Q14397
Target protein
KP13_00117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 522.47 Da
LogP (Crippen) 2.88
H-bond donors 2
H-bond acceptors 6
TPSA 99.76 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.38
Formula C₂₁H₂₀F₆N₄O₃S

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 99.8
  • −1 ≤ LogP ≤ 5 2.88
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 522.5
  • LogP ≤ 5 2.88
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 99.8
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 
CC#CC1CN(CCN1c2ccc(cc2)C(C(F)(F)F)(C(F)(F)F)O)S(=O)(=O)c3ccc(nc3)N
InChI 
InChI=1S/C21H20F6N4O3S/c1-2-3-16-13-30(35(33,34)17-8-9-18(28)29-12-17)10-11-31(16)15-6-4-14(5-7-15)19(32,20(22,23)24)21(25,26)27/h4-9,12,16,32H,10-11,13H2,1H3,(H2,28,29)
InChIKey 
SIFKNECWLVONIH-UHFFFAOYSA-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)