SMTL ID : 6q6l.1

Crystal structure of recombinant human beta-glucocerebrosidase in complex with adamantyl-cyclophellitol inhibitor (ME656)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

1 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 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

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

19 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 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: K.473 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Ligands: RJR.13, ACT.21 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: S.464, S.465, Y.487 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: E.111, R.170, P.428 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: H.274, N.275 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: R.277, V.305, H.306 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain B: S.464, S.465, Y.487 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: A.1, R.2, S.25 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain B: L.165, R.170, P.171, V.172 Ligand excluded by PLIP

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

ACT.8: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP ACT.9: 2 residues within 4Å: Chain A: R.329, L.330 Ligand excluded by PLIP ACT.10: 1 residues within 4Å: Ligands: RJR.36 Ligand excluded by PLIP ACT.19: 1 residues within 4Å: Chain A: A.1 Ligand excluded by PLIP ACT.20: 4 residues within 4Å: Chain A: D.24, S.25, F.26, R.48 Ligand excluded by PLIP ACT.21: 7 residues within 4Å: Chain A: E.235, S.237, A.238, Y.244, D.283, Q.284 Ligands: SO4.12 Ligand excluded by PLIP ACT.22: 2 residues within 4Å: Chain A: S.45, R.47 Ligand excluded by PLIP ACT.23: 2 residues within 4Å: Chain A: K.198, G.199 Ligand excluded by PLIP ACT.24: 4 residues within 4Å: Chain A: Q.226, H.273, N.275, V.276 Ligand excluded by PLIP ACT.25: 4 residues within 4Å: Chain A: R.285, P.319, A.320, T.369 Ligand excluded by PLIP ACT.26: 3 residues within 4Å: Chain A: I.158, P.159, H.162 Ligand excluded by PLIP ACT.31: 2 residues within 4Å: Chain B: K.198, G.199 Ligand excluded by PLIP ACT.32: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP ACT.33: 2 residues within 4Å: Chain B: E.254, R.257 Ligand excluded by PLIP ACT.34: 2 residues within 4Å: Chain B: R.44, Y.487 Ligand excluded by PLIP ACT.40: 3 residues within 4Å: Chain B: P.289, H.290, K.293 Ligand excluded by PLIP ACT.41: 5 residues within 4Å: Chain B: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP ACT.42: 2 residues within 4Å: Chain B: Q.207, R.211 Ligand excluded by PLIP ACT.43: 2 residues within 4Å: Chain B: H.274, N.275 Ligand excluded by PLIP ACT.44: 2 residues within 4Å: Chain B: R.277, H.306 Ligand excluded by PLIP ACT.45: 4 residues within 4Å: Chain B: L.67, A.438, N.442, L.444 Ligand excluded by PLIP ACT.46: 6 residues within 4Å: Chain B: Y.313, L.314, D.315, C.342, V.343 Ligands: RJR.36 Ligand excluded by PLIP ACT.47: 1 residues within 4Å: Chain B: K.155 Ligand excluded by PLIP ACT.48: 2 residues within 4Å: Chain B: S.45, R.47 Ligand excluded by PLIP

2 x RJR: (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[4-[3-(1-adamantylmethoxy)propyl]-1,2,3-triazol-1-yl]methyl]cyclohexane-1,2,3,5-tetrol(Covalent)

RJR.13: 17 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, L.241, F.246, Y.313, E.340, W.381, N.396, F.397, V.398 Chain B: D.315, F.316, K.346 Ligands: SO4.12 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.241, A:E.340, B:F.316, B:F.316 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.235, A:E.235, A:N.396, A:F.397 Water bridges: A:E.235 RJR.36: 20 residues within 4Å: Chain A: F.316, L.317, F.347 Chain B: D.127, F.128, W.179, N.234, E.235, F.246, Q.284, W.312, Y.313, F.316, E.340, C.342, W.381, N.396, V.398 Ligands: ACT.10, ACT.46 20 PLIP interactions: 3 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:F.316, A:L.317, A:F.347, B:Q.284, B:W.312, B:W.312, B:Y.313, B:Y.313, B:Y.313, B:Y.313, B:Y.313, B:F.316, B:E.340 Hydrogen bonds: B:D.127, B:W.179, B:N.234, B:E.235, B:Y.313, B:N.396 Water bridges: B:E.235

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

NAG.35: 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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