7NI3 | pdb_00007ni3

CRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH CPD 3

PDB DOI: https://doi.org/10.2210/pdb7NI3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2021-02-11 Released: 2022-02-23
Deposition Author(s): Sjogren, T., Inghardt, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.224 (Depositor), 0.235 (DCC)
R-Value Work:
0.175 (Depositor), 0.182 (DCC)
R-Value Observed:
0.177 (Depositor)

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

PubMed: 36005476 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.1c02141
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 135.12 kDa
Atom Count: 10,213
Modeled Residue Count: 1,136
Deposited Residue Count: 1,142
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase	A, B	105	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05164
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase	C, D	466	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05164
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C Focus chain D	Go to GlyGen: P05164-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	4		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
UE8 (Subject of Investigation/LOI) Query on UE8 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain S [auth D] mmCIF format, chain M [auth C] mmCIF format, chain S [auth D]	M [auth C], S [auth D]	2-sulfanylidene-3-[(2R)-tetrahydro-2-furanylmethyl]-1,2,3,7-tetrahydro-6H-purin-6-one C₁₀ H₁₂ N₄ O₂ S RSPDBEVKURKEII-ZCFIWIBFSA-N		Interactions Focus chain M [auth C] Focus chain S [auth D] Interactions & Density Focus chain M [auth C] Focus chain S [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	P [auth C], Q [auth C], U [auth D], V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C]	R [auth C], T [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain R [auth C] Focus chain T [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain W [auth D] MOL2 format, chain N [auth C] MOL2 format, chain W [auth D] mmCIF format, chain N [auth C] mmCIF format, chain W [auth D]	N [auth C], W [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain W [auth D] Interactions & Density Focus chain N [auth C] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain O [auth C] SDF format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth C] MOL2 format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth C] mmCIF format, chain H [auth A]	H [auth A], I [auth B], K [auth B], L [auth C], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain O [auth C]