SMTL ID : 8f97.1 (1 other biounit)

Compound 5 bound to procaspase-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

1 x XM6: 2-({[(2M)-[2,3'-bipyridin]-2'-yl]amino}methyl)-5-fluorophenol(Non-covalent)

XM6.1: 11 residues within 4Å: Chain A: A.195, S.196, V.197, Y.198, T.199, L.200, E.214 Chain B: Y.198, T.199, L.200, P.201 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.198, A:L.200, A:E.214, B:Y.198 Hydrogen bonds: A:T.199 pi-Stacking: A:Y.198, A:Y.198, B:Y.198 Water bridges: B:N.125

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: T.190, W.227, C.264 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.190, A:W.227 EDO.3: 3 residues within 4Å: Chain B: D.90, K.92, Y.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.95 EDO.4: 2 residues within 4Å: Chain B: W.57, H.58 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.57

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: E.214, G.215, Y.216 Chain B: K.144, D.146, A.202 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.202, A:Y.216 Water bridges: B:D.146, A:Y.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Togo, T. et al., Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6. J.Med.Chem. (2023)

Release Date

2023-12-13

Peptides

Procaspase-6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Procaspase-6

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