7NI1

CRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH CPD 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Discovery of AZD4831, a Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As a Potential Treatment for Heart Failure with Preserved Ejection Fraction.

Inghardt, T.Antonsson, T.Ericsson, C.Hovdal, D.Johannesson, P.Johansson, C.Jurva, U.Kajanus, J.Kull, B.Michaelsson, E.Pettersen, A.Sjogren, T.Sorensen, H.Westerlund, K.Lindstedt, E.L.

(2022) J Med Chem 65: 11485-11496

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02141
  • Primary Citation of Related Structures:  
    7NI1, 7NI3

  • PubMed Abstract: 

    Myeloperoxidase is a promising therapeutic target for treatment of patients suffering from heart failure with preserved ejection fraction (HFpEF). We aimed to discover a covalent myeloperoxidase inhibitor with high selectivity for myeloperoxidase over thyroid peroxidase, limited penetration of the blood-brain barrier, and pharmacokinetics suitable for once-daily oral administration at low dose. Structure-activity relationship, biophysical, and structural studies led to prioritization of four compounds for in-depth safety and pharmacokinetic studies in animal models. One compound (AZD4831) progressed to clinical studies on grounds of high potency (IC 50 , 1.5 nM in vitro ) and selectivity (>450-fold vs thyroid peroxidase in vitro ), the mechanism of irreversible inhibition, and the safety profile. Following phase 1 studies in healthy volunteers and a phase 2a study in patients with HFpEF, a phase 2 b /3 efficacy study of AZD4831 in patients with HFpEF started in 2021.


  • Organizational Affiliation

    Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloperoxidase
A, B
105Homo sapiensMutation(s): 0 
EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens)
Explore P05164 
Go to UniProtKB:  P05164
PHAROS:  P05164
GTEx:  ENSG00000005381 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05164
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloperoxidase
C, D
466Homo sapiensMutation(s): 0 
EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens)
Explore P05164 
Go to UniProtKB:  P05164
PHAROS:  P05164
GTEx:  ENSG00000005381 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05164
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P05164-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF
GlyCosmos:  G42466VF
GlyGen:  G42466VF
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UEB (Subject of Investigation/LOI)
Query on UEB

Download Ideal Coordinates CCD File 
R [auth C],
Y [auth D]
(S)-1-(2-(amino(phenyl)methyl)benzyl)-2-thioxo-1,2,3,5-tetrahydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
C20 H18 N4 O S
JABFRGYJMKKWKF-QGZVFWFLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
P [auth C],
Q [auth C],
V [auth D],
W [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
S [auth C],
T [auth D]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth C],
X [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth B]
N [auth C]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
U [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
UEB BindingDB:  7NI1 Kd: 631 (nM) from 1 assay(s)
IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.22α = 90
b = 63.82β = 97.24
c = 111.34γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2022-08-31
    Changes: Database references
  • Version 1.3: 2022-09-07
    Changes: Database references
  • Version 1.4: 2022-09-21
    Changes: Database references
  • Version 1.5: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-11-13
    Changes: Structure summary