SMTL ID : 8xgy.1

Crystal structure of human Golgi resident glutaminyl cyclase in complex with (R,Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-((1-acetylpyrrolidin-3-yl)oxy)indolin-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.127, E.170, H.298 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.127, A:E.170, A:H.298 ZN.3: 4 residues within 4Å: Chain B: D.127, E.170, H.298 Ligands: 01.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.127, B:E.170, B:H.298 ZN.5: 4 residues within 4Å: Chain C: D.127, E.170, H.298 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.127, C:D.127, C:E.170, C:H.298 ZN.7: 4 residues within 4Å: Chain D: D.127, E.170, H.298 Ligands: 01.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.127, D:E.170, D:H.298 ZN.9: 4 residues within 4Å: Chain E: D.127, E.170, H.298 Ligands: 01.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.127, E:E.170, E:H.298 ZN.11: 4 residues within 4Å: Chain F: D.127, E.170, H.298 Ligands: 01.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.127, F:E.170, F:H.298 ZN.13: 4 residues within 4Å: Chain G: D.127, E.170, H.298 Ligands: 01.14 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.127, G:E.170, G:H.298 ZN.15: 4 residues within 4Å: Chain H: D.127, E.170, H.298 Ligands: 01.16 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.127, H:E.170, H:H.298 ZN.17: 4 residues within 4Å: Chain I: D.127, E.170, H.298 Ligands: 01.18 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.127, I:E.170, I:H.298 ZN.19: 4 residues within 4Å: Chain J: D.127, E.170, H.298 Ligands: 01.20 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:D.127, J:E.170, J:H.298 ZN.21: 4 residues within 4Å: Chain K: D.127, E.170, H.298 Ligands: 01.22 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.127, K:E.170, K:H.298 ZN.23: 5 residues within 4Å: Chain L: D.127, E.170, W.297, H.298 Ligands: 01.24 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.127, L:E.170, L:H.298

12 x 01: (3~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-[(3~{R})-1-ethanoylpyrrolidin-3-yl]oxy-1~{H}-indol-2-one

01.2: 17 residues within 4Å: Chain A: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, S.291, F.293, W.297, H.298 Chain E: P.230, N.231 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.175, A:F.293, A:W.297 Hydrogen bonds: A:D.216 pi-Stacking: A:W.175, A:F.293, A:W.297 01.4: 15 residues within 4Å: Chain B: D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, F.293, W.297, H.298 Chain D: P.230, N.231 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.175, B:F.293, B:W.297 Hydrogen bonds: B:D.216, B:Y.267 pi-Stacking: B:W.175, B:W.297 01.6: 17 residues within 4Å: Chain B: P.230, N.231 Chain C: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, S.291, F.293, W.297, H.298 Ligands: ZN.5 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.271, C:W.297, B:P.230 Hydrogen bonds: C:Y.267 pi-Stacking: C:W.175, C:W.297 01.8: 16 residues within 4Å: Chain C: F.228, P.230, N.231 Chain D: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, W.297, H.298 Ligands: ZN.7 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.175, C:N.231 Hydrogen bonds: D:D.216, D:Y.267 pi-Stacking: D:W.175, D:W.297 01.10: 16 residues within 4Å: Chain E: D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, F.293, W.297, H.298 Chain K: P.230, N.231, Y.267 Ligands: ZN.9 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain K Hydrophobic interactions: E:W.175, E:I.271, E:F.293, E:W.297, K:N.231 Hydrogen bonds: E:Y.267 pi-Stacking: E:W.175, E:W.297 01.12: 16 residues within 4Å: Chain F: D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, F.293, W.297, H.298 Chain I: F.228, P.230, N.231 Ligands: ZN.11 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.293, F:W.297 Hydrogen bonds: F:D.216, F:Y.267 pi-Stacking: F:W.175, F:W.175, F:F.293, F:W.297 01.14: 17 residues within 4Å: Chain G: H.108, K.112, D.127, E.169, E.170, W.175, D.216, L.217, V.270, I.271, Q.272, W.297, H.298 Chain J: F.228, F.229, N.231 Ligands: ZN.13 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain J Hydrophobic interactions: G:W.175, G:I.271, G:I.271, J:N.231 Hydrogen bonds: G:K.112, G:K.112, G:D.216 pi-Stacking: G:W.175, G:W.297 01.16: 16 residues within 4Å: Chain F: F.228, P.230, N.231 Chain H: D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, F.293, W.297, H.298 Ligands: ZN.15 11 PLIP interactions: 9 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: H:I.271, H:F.293, H:W.297, F:P.230, F:N.231 Hydrogen bonds: H:D.216, H:W.297 pi-Stacking: H:W.175, H:F.293, H:W.297, H:W.297 01.18: 18 residues within 4Å: Chain H: F.228, P.230, N.231 Chain I: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, V.270, I.271, Q.272, D.273, W.297, H.298 Ligands: ZN.17 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:W.175, I:W.175, I:W.175, I:W.297 pi-Stacking: I:W.297 01.20: 18 residues within 4Å: Chain J: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, V.270, I.271, Q.272, D.273, W.297, H.298 Chain L: F.228, P.230, N.231 Ligands: ZN.19 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: J:W.175, J:W.297, L:P.230, L:N.231 pi-Stacking: J:W.175, J:F.293, J:W.297 01.22: 14 residues within 4Å: Chain A: F.228, P.230, N.231 Chain K: H.108, D.127, E.169, E.170, W.175, D.216, Q.272, F.293, W.297, H.298 Ligands: ZN.21 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:W.175, K:F.293 Hydrogen bonds: K:D.216 pi-Stacking: K:W.175, K:W.297 01.24: 18 residues within 4Å: Chain G: F.228, F.229, N.231, G.268, G.269 Chain L: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, W.297, H.298 Ligands: ZN.23 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:W.297 Hydrogen bonds: L:D.216 pi-Stacking: L:W.175, L:F.293, L:W.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mou, J. et al., X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model. J.Med.Chem. (2024)

Release Date

2024-06-12

Peptides

Glutaminyl-peptide cyclotransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Glutaminyl-peptide cyclotransferase

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