SMTL ID : 6jf0.1

Covalent labeling of hPPARg-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

1 x EB6: methyl (2~{S})-3-[4-[3-(4-methoxy-2-oxidanyl-phenyl)prop-2-ynoyloxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoate(Non-covalent)

EB6.1: 19 residues within 4Å: Chain A: F.81, G.83, C.84, Q.85, R.87, S.88, H.122, I.125, L.129, V.138, I.140, L.152, L.155, F.159, F.162, M.163, H.248, L.268, Y.272 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.81, A:Q.85, A:R.87, A:R.87, A:I.125, A:L.129, A:L.152, A:L.155, A:F.162, A:F.162, A:F.162, A:F.162, A:M.163 Salt bridges: A:H.122, A:H.248 pi-Stacking: A:F.81

1 x EBF: 7-methoxychromen-2-one(Covalent)

EBF.2: 6 residues within 4Å: Chain B: G.83, C.84, R.87, L.129, I.140, S.141 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.87, B:I.140 Hydrogen bonds: B:S.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kojima, H. et al., Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins. Cell Chem Biol (2020)

Release Date

2020-02-12

Peptides

Peroxisome proliferator-activated receptor gamma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxisome proliferator-activated receptor gamma

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