8XFV | pdb_00008xfv

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 
    0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XFV

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model.

Mou, J.Ning, X.L.Wang, X.Y.Hou, S.Y.Meng, F.B.Zhou, C.Wu, J.W.Li, C.Jia, T.Wu, X.Wu, Y.Chen, Y.Li, G.B.

(2024) J Med Chem 67: 8730-8756

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00049
  • Primary Citation Related Structures: 
    8XFV, 8XGA, 8XGB, 8XGT, 8XGY

  • PubMed Abstract: 

    The secretory glutaminyl cyclase (sQC) and Golgi-resident glutaminyl cyclase (gQC) are responsible for N-terminal protein pyroglutamation and associated with various human diseases. Although several sQC/gQC inhibitors have been reported, only one inhibitor, PQ912, is currently undergoing clinic trials for the treatment of Alzheimer's disease. We report an X-ray crystal structure of sQC complexed with PQ912, revealing that the benzimidazole makes "anchor" interactions with the active site zinc ion and catalytic triad. Structure-guided design and optimization led to a series of new benzimidazole derivatives exhibiting nanomolar inhibition for both sQC and gQC. In a MPTP-induced Parkinson's disease (PD) mouse model, BI-43 manifested efficacy in mitigating locomotor deficits through reversing dopaminergic neuronal loss, reducing microglia, and decreasing levels of the sQC/gQC substrates, α-synuclein, and CCL2. This study not only offers structural basis and new leads for drug discovery targeting sQC/gQC but also provides evidence supporting sQC/gQC as potential targets for PD treatment.


  • Organizational Affiliation
    • Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 389.57 kDa 
  • Atom Count: 27,523 
  • Modeled Residue Count: 3,443 
  • Deposited Residue Count: 3,443 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutaminyl-peptide cyclotransferase-like protein313Homo sapiensMutation(s): 0 
Gene Names: QPCTL
EC: 2.3.2.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXS2 (Homo sapiens)
Explore Q9NXS2 
Go to UniProtKB:  Q9NXS2
PHAROS:  Q9NXS2
GTEx:  ENSG00000011478 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXS2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D46
(Subject of Investigation/LOI)

Query on A1D46



Download:Ideal Coordinates CCD File
AA [auth G]
CA [auth H]
EA [auth I]
GA [auth J]
M [auth X]
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
M [auth X],
O [auth A],
Q [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F]
3-(1~{H}-benzimidazol-5-ylmethylidene)-4-piperidin-4-yloxy-1~{H}-indol-2-one
C21 H20 N4 O2
GEWYCLDNMSKZLN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BA [auth H]
DA [auth I]
FA [auth J]
L [auth X]
N [auth A]
BA [auth H],
DA [auth I],
FA [auth J],
L [auth X],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free:  0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.279α = 90
b = 109.126β = 104.73
c = 159.537γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82122065;82073698

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary