SMTL ID : 5lvx.1

Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: R.2, I.5, N.19, T.21, Y.22 Chain C: E.41, T.43, R.44, S.45, R.47, S.465, D.467, P.485, G.486 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.41, C:S.45 Hydrophobic interactions: A:Y.22 NAG-NAG-BMA-MAN-MAN-MAN.4: 13 residues within 4Å: Chain B: E.41, T.43, S.45, R.47, S.465, D.467, P.485, G.486 Chain D: R.2, I.5, N.19, T.21, Y.22 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.41, B:S.45, B:R.47 Hydrophobic interactions: D:Y.22

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.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

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 4 residues within 4Å: Chain C: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP)

2 x 79B: 11-[(2~{R})-2-[(2-pyridin-3-ylquinazolin-4-yl)amino]-2,3-dihydro-1~{H}-inden-5-yl]undec-10-ynoic acid(Covalent)

79B.5: 13 residues within 4Å: Chain A: E.235, S.237, D.283, Q.284, Y.313, L.314, F.316, E.340, C.342, S.345, K.346, W.348 Chain B: L.241 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:L.241, A:Y.313, A:F.316, A:F.316, A:F.316, A:F.316, A:W.348, A:W.348 Hydrogen bonds: A:Q.284, A:S.345, A:S.345 pi-Stacking: A:Y.313, A:Y.313 79B.26: 13 residues within 4Å: Chain C: L.241 Chain D: E.235, S.237, Y.244, Q.284, Y.313, L.314, F.316, E.340, S.345, K.346, W.348, N.396 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.313, D:F.316, D:F.316, D:F.316, D:F.316, D:K.346, D:W.348, D:W.348, C:L.241 Hydrogen bonds: D:Q.284, D:S.345, D:S.345 pi-Stacking: D:Y.313, D:Y.313

21 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 2 residues within 4Å: Chain A: R.353 Chain C: K.408 Ligand excluded by PLIP PO4.7: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP PO4.8: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.9: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.10: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP PO4.11: 4 residues within 4Å: Chain A: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.14: 2 residues within 4Å: Chain B: R.277, H.306 Ligand excluded by PLIP PO4.15: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.17: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.18: 5 residues within 4Å: Chain B: K.321, G.325, R.329, Y.373, H.374 Ligand excluded by PLIP PO4.20: 2 residues within 4Å: Chain C: H.290, K.293 Ligand excluded by PLIP PO4.21: 6 residues within 4Å: Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.22: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain C: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.24: 3 residues within 4Å: Chain C: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.27: 4 residues within 4Å: Chain D: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.28: 2 residues within 4Å: Chain D: R.44, S.45 Ligand excluded by PLIP PO4.29: 6 residues within 4Å: Chain D: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.31: 2 residues within 4Å: Chain B: K.408 Chain D: R.353 Ligand excluded by PLIP

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

NAG.12: 3 residues within 4Å: Chain B: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain D: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP)

2 x 7E4: 11-[(2~{S})-2-[(2-pyridin-3-ylquinazolin-4-yl)amino]-2,3-dihydro-1~{H}-inden-5-yl]undec-10-ynoic acid(Covalent)

7E4.13: 18 residues within 4Å: Chain A: L.241, S.242, G.243, Y.244, F.347 Chain B: E.235, S.237, Y.244, Q.284, Y.313, L.314, F.316, E.340, C.342, S.345, K.346, W.348, N.396 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.313, B:F.316, B:F.316, B:F.316, B:W.348, B:W.348, A:L.241, A:F.347, A:F.347, A:F.347 Hydrogen bonds: B:Y.244, B:S.345, B:S.345 pi-Stacking: B:Y.313, B:Y.313 7E4.19: 17 residues within 4Å: Chain C: E.235, S.237, Y.244, Q.284, Y.313, L.314, F.316, E.340, C.342, S.345, K.346, W.348, N.396 Chain D: S.242, G.243, P.245, F.347 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.313, C:F.316, C:F.316, C:F.316, C:W.348, D:F.347, D:F.347, D:F.347 Hydrogen bonds: C:Q.284, C:S.345, C:S.345 pi-Stacking: C:Y.313, C:Y.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, J. et al., beta-Glucocerebrosidase Modulators Promote Dimerization of beta-Glucocerebrosidase and Reveal an Allosteric Binding Site. J. Am. Chem. Soc. (2018)

Release Date

2017-10-25

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucosylceramidase

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