SMTL ID : 6q6n.1

Crystal structure of recombinant human beta-glucocerebrosidase in complex with biphenyl-cyclophellitol inhibitor (ME655)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.22 Water bridges: A:R.2 NAG-NAG.2: 4 residues within 4Å: Chain B: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.22 Water bridges: B:R.2

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:W.357, A:D.358 Water bridges: A:E.349, A:R.353, A:R.353, A:S.356 Salt bridges: A:R.353 SO4.4: 2 residues within 4Å: Chain A: R.44, S.45 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44, A:S.45 Salt bridges: A:R.44 SO4.5: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.79, A:K.79, A:R.277, A:R.277 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.6: 3 residues within 4Å: Chain A: T.63, G.64, Q.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.440, A:Q.440 SO4.7: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.11, A:Y.11, A:W.348, A:Q.350 Water bridges: A:R.353 Salt bridges: A:R.353 SO4.9: 2 residues within 4Å: Chain A: R.329, L.330 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.329 SO4.12: 2 residues within 4Å: Chain A: E.254, R.257 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.257 Salt bridges: A:R.257 SO4.16: 2 residues within 4Å: Chain A: H.290, K.293 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.290, A:K.293 SO4.18: 3 residues within 4Å: Chain A: T.43, S.45, R.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.43, A:T.43, A:S.45 Salt bridges: A:R.47 SO4.26: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:W.357, B:D.358 Water bridges: B:E.349, B:E.349, B:R.353, B:S.356 Salt bridges: B:R.353 SO4.27: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 8 PLIP interactions: 8 interactions with chain B Water bridges: B:K.79, B:W.228, B:R.277, B:R.277, B:H.306 Salt bridges: B:K.79, B:R.277, B:H.306 SO4.28: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.194, B:G.243 SO4.29: 2 residues within 4Å: Chain B: R.44, S.45 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.44, B:S.45 Salt bridges: B:R.44 SO4.37: 3 residues within 4Å: Chain B: A.1, R.2, S.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.25, B:S.25 Salt bridges: B:R.2 SO4.43: 3 residues within 4Å: Chain B: L.165, P.171, V.172 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.172 Water bridges: B:L.165, B:A.168, B:V.172

24 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 2 residues within 4Å: Chain A: R.44, Y.487 Ligand excluded by PLIP ACT.10: 3 residues within 4Å: Chain A: E.111, R.170, P.428 Ligand excluded by PLIP ACT.11: 2 residues within 4Å: Chain A: T.252, H.255 Ligand excluded by PLIP ACT.13: 4 residues within 4Å: Chain A: Q.226, H.273, N.275, V.276 Ligand excluded by PLIP ACT.14: 2 residues within 4Å: Chain A: H.274, N.275 Ligand excluded by PLIP ACT.15: 3 residues within 4Å: Chain A: F.75, H.328, H.374 Ligand excluded by PLIP ACT.17: 2 residues within 4Å: Chain A: Q.207, R.211 Ligand excluded by PLIP ACT.19: 2 residues within 4Å: Chain A: A.438, N.442 Ligand excluded by PLIP ACT.21: 3 residues within 4Å: Chain A: R.277, V.305, H.306 Ligand excluded by PLIP ACT.22: 3 residues within 4Å: Chain A: T.187, K.198, G.199 Ligand excluded by PLIP ACT.23: 4 residues within 4Å: Chain A: R.285, P.319, A.320, T.369 Ligand excluded by PLIP ACT.24: 5 residues within 4Å: Chain A: F.31, S.455, L.493, W.494, H.495 Ligand excluded by PLIP ACT.25: 4 residues within 4Å: Chain A: W.312, Y.313, C.342, Q.362 Ligand excluded by PLIP ACT.30: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP ACT.31: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP ACT.32: 5 residues within 4Å: Chain B: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP ACT.33: 2 residues within 4Å: Chain B: H.290, K.293 Ligand excluded by PLIP ACT.34: 1 residues within 4Å: Chain B: R.262 Ligand excluded by PLIP ACT.35: 3 residues within 4Å: Chain B: S.464, S.465, Y.487 Ligand excluded by PLIP ACT.36: 5 residues within 4Å: Chain B: L.67, L.436, A.438, N.442, L.444 Ligand excluded by PLIP ACT.38: 2 residues within 4Å: Chain B: E.254, R.257 Ligand excluded by PLIP ACT.39: 1 residues within 4Å: Chain B: R.277 Ligand excluded by PLIP ACT.40: 1 residues within 4Å: Chain B: Q.207 Ligand excluded by PLIP ACT.44: 3 residues within 4Å: Chain B: D.315, W.348, E.349 Ligand excluded by PLIP

2 x HK2: (1~{S},3~{S},4~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-[[4-[3-(4-phenylphenoxy)propyl]-1,2,3-triazol-1-yl]methyl]cyclohexan-1-olate(Covalent)

HK2.20: 11 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, C.342, W.381, N.396 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.313, A:Y.313, A:E.340 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.235, A:Y.313, A:N.396 Water bridges: A:E.235 HK2.42: 13 residues within 4Å: Chain B: D.127, F.128, W.179, N.234, E.235, F.246, D.315, E.340, C.342, V.343, W.381, N.396, V.398 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.340 Hydrogen bonds: B:D.127, B:W.179, B:N.234, B:E.235, B:N.396 Water bridges: B:E.235, B:E.235, B:E.235

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.41: 2 residues within 4Å: Chain B: H.145, N.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Artola, M. et al., Functionalized Cyclophellitols Are Selective Glucocerebrosidase Inhibitors and Induce a Bona Fide Neuropathic Gaucher Model in Zebrafish. J.Am.Chem.Soc. (2019)

Release Date

2019-03-27

Peptides

Glucosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucosylceramidase

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