SMTL ID : 8f97.2 (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: 10 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 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: 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

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

EDO.2: 3 residues within 4Å: Chain A: D.90, E.95, Y.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.95 EDO.3: 3 residues within 4Å: Chain A: F.56, W.57, H.58 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.57 EDO.4: 5 residues within 4Å: Chain A: M.39, D.40, H.41, K.291, S.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.39, A:S.292, A:S.292 EDO.5: 3 residues within 4Å: Chain B: F.56, W.57, H.58 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain B: L.81, P.290, K.291 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: M.39, D.40, H.41, R.42, K.291, S.292, N.293, L.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.39, B:R.42, B:K.291, B:S.292

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
C

B
D

Procaspase-6

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