6WY7

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-41 A.K.A 7-[1-phenyl-3-({4-phenylbicyclo[2.2.2]octan-1-yl}amino)propyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and structure activity relationships of 7-benzyl triazolopyridines as stable, selective, and reversible inhibitors of myeloperoxidase.

Shaw, S.A.Vokits, B.P.Dilger, A.K.Viet, A.Clark, C.G.Abell, L.M.Locke, G.A.Duke, G.Kopcho, L.M.Dongre, A.Gao, J.Krishnakumar, A.Jusuf, S.Khan, J.Spronk, S.A.Basso, M.D.Zhao, L.Cantor, G.H.Onorato, J.M.Wexler, R.R.Duclos, F.Kick, E.K.

(2020) Bioorg Med Chem 28: 115723-115723

  • DOI: https://doi.org/10.1016/j.bmc.2020.115723
  • Primary Citation of Related Structures:  
    6WXZ, 6WY0, 6WY5, 6WY7, 6WYD

  • PubMed Abstract: 

    Myeloperoxidase (MPO) is a heme peroxidase found in neutrophils, monocytes and macrophages that efficiently catalyzes the oxidation of endogenous chloride into hypochlorous acid for antimicrobial activity. Chronic MPO activation can lead to indiscriminate protein modification causing tissue damage, and has been associated with chronic inflammatory diseases, atherosclerosis, and acute cardiovascular events. Triazolopyrimidine 5 is a reversible MPO inhibitor; however it suffers from poor stability in acid, and is an irreversible inhibitor of the DNA repair protein methyl guanine methyl transferase (MGMT). Structure-based drug design was employed to discover benzyl triazolopyridines with improved MPO potency, as well as acid stability, no reactivity with MGMT, and selectivity against thyroid peroxidase (TPO). Structure-activity relationships, a crystal structure of the MPO-inhibitor complex, and acute in vivo pharmacodynamic data are described herein.


  • Organizational Affiliation

    Bristol Myers Squibb Company, P.O. Box 5400, Princeton, NJ 08543-5400, United States. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloperoxidase light chainA,
C [auth D]
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 heavy chainB,
D [auth E]
467Homo 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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseE [auth C],
F
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
H [auth B],
N [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
UFD (Subject of Investigation/LOI)
Query on UFD

Download Ideal Coordinates CCD File 
M [auth B],
R [auth E]
7-{(1R)-1-phenyl-3-[(4-phenylbicyclo[2.2.2]octan-1-yl)amino]propyl}-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
C28 H32 N6
XBWRTBUYSVKILQ-OFEZKSIWSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
O [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth B],
P [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
B,
D [auth E]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
UFD BindingDB:  6WY7 IC50: min: 1, max: 1.4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.998α = 90
b = 104.998β = 90
c = 223.998γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-10-14 
  • Deposition Author(s): Khan, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection