SMTL ID : 8xgt.1

Crystal structure of human secretory glutaminyl cyclase in complex with (Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-hydroxyindolin-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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.127, A:D.127, A:E.170, A:E.170, A:H.298 ZN.3: 4 residues within 4Å: Chain B: D.127, E.170, H.298 Ligands: 01.4 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.127, B:D.127, B:E.170, B:E.170, B:H.298 ZN.5: 4 residues within 4Å: Chain C: D.127, E.170, H.298 Ligands: 01.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.127, C:D.127, C:E.170, C:E.170, C:H.298 ZN.7: 4 residues within 4Å: Chain D: D.127, E.170, H.298 Ligands: 01.8 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.127, D:D.127, D:E.170, D:E.170, D:H.298 ZN.9: 4 residues within 4Å: Chain E: D.127, E.170, H.298 Ligands: 01.10 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.127, E:E.170, E:E.170, E:H.298 ZN.11: 4 residues within 4Å: Chain F: D.127, E.170, H.298 Ligands: 01.12 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.127, F:D.127, F:E.170, F:E.170, F:H.298 ZN.13: 4 residues within 4Å: Chain G: D.127, E.170, H.298 Ligands: 01.14 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.127, G:D.127, G:E.170, G:E.170, G:H.298 ZN.15: 4 residues within 4Å: Chain H: D.127, E.170, H.298 Ligands: 01.16 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.127, H:E.170, H:E.170, H:H.298 ZN.17: 4 residues within 4Å: Chain I: D.127, E.170, H.298 Ligands: 01.18 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.127, 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 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.127, J:E.170, J:E.170, J:H.298 ZN.21: 4 residues within 4Å: Chain K: D.127, E.170, H.298 Ligands: 01.22 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.127, K:E.170, K:E.170, K:H.298 ZN.23: 4 residues within 4Å: Chain L: D.127, E.170, H.298 Ligands: 01.24 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.127, L:E.170, L:E.170, L:H.298

12 x 01: (3~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-oxidanyl-1~{H}-indol-2-one

01.2: 13 residues within 4Å: Chain A: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Chain E: P.230, N.231 Ligands: ZN.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:W.175, A:W.297, E:P.230, E:N.231 pi-Stacking: A:W.175, A:W.175, A:F.293, A:W.297 01.4: 12 residues within 4Å: Chain B: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, D.273, W.297, H.298 Chain D: N.231 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.175, B:W.297 pi-Stacking: B:W.175, B:W.297 01.6: 12 residues within 4Å: Chain B: P.230, N.231 Chain C: H.108, D.127, E.169, E.170, W.175, D.216, Q.272, W.297, H.298 Ligands: ZN.5 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.297, B:N.231 pi-Stacking: C:W.175, C:W.297 01.8: 13 residues within 4Å: Chain C: P.230, N.231 Chain D: H.108, D.127, E.169, E.170, W.175, D.216, L.217, 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, D:W.297, C:N.231 Hydrogen bonds: D:E.169 pi-Stacking: D:W.175, D:W.297 01.10: 13 residues within 4Å: Chain E: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, F.293, W.297, H.298 Chain K: P.230, N.231 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.297 pi-Stacking: E:W.175, E:F.293, E:W.297 01.12: 12 residues within 4Å: Chain F: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, D.273, W.297, H.298 Chain I: N.231 Ligands: ZN.11 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:W.175, F:W.297 pi-Stacking: F:W.175, F:W.175, F:F.293, F:W.297 01.14: 15 residues within 4Å: Chain G: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, W.297, H.298 Chain J: P.230, N.231 Ligands: ZN.13 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:W.175, G:I.271 pi-Stacking: G:W.175, G:W.175, G:W.175, G:W.297 01.16: 12 residues within 4Å: Chain F: P.230, N.231 Chain H: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Ligands: ZN.15 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: H:W.297, F:P.230 Hydrogen bonds: H:H.298 pi-Stacking: H:W.175, H:F.293, H:W.297 01.18: 14 residues within 4Å: Chain H: P.230, N.231 Chain I: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Q.272, D.273, W.297, H.298 Ligands: ZN.17 7 PLIP interactions: 1 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:N.231, I:W.175, I:W.175, I:W.175, I:W.297 pi-Stacking: I:F.293, I:W.297 01.20: 13 residues within 4Å: Chain J: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Q.272, D.273, W.297, H.298 Chain L: N.231 Ligands: ZN.19 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:W.175, J:W.175, J:W.175, J:W.297 pi-Stacking: J:W.175, J:W.175, J:W.297 01.22: 14 residues within 4Å: Chain A: P.230, N.231 Chain K: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Q.272, D.273, W.297, H.298 Ligands: ZN.21 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:W.175, K:W.297, A:P.230 pi-Stacking: K:W.175, K:F.293, K:W.297 01.24: 13 residues within 4Å: Chain G: P.230, N.231 Chain L: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:W.175, L:W.297 pi-Stacking: L:W.175, 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

Related Entries With Identical Sequence