5QJ2

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) OMPLEX WITH COMPOUND-20 AKA 7-((3-(1-METHYL-1H-PYRAZOL-3- YL)BENZYL)OXY)- 1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Potent Triazolopyridine Myeloperoxidase Inhibitors.

Wurtz, N.R.Viet, A.Shaw, S.A.Dilger, A.Valente, M.N.Khan, J.A.Jusuf, S.Narayanan, R.Fernando, G.Lo, F.Liu, X.Locke, G.A.Kopcho, L.Abell, L.M.Sleph, P.Basso, M.Zhao, L.Wexler, R.R.Duclos, F.Kick, E.K.

(2018) ACS Med Chem Lett 9: 1175-1180

  • DOI: 10.1021/acsmedchemlett.8b00308
  • Primary Citation of Related Structures:  
    5QJ2, 5QJ3

  • PubMed Abstract: 
  • Myeloperoxidase (MPO) generates reactive oxygen species that potentially contribute to many chronic inflammatory diseases. A recently reported triazolopyrimidine MPO inhibitor was optimized to improve acid stability and remove methyl guanine methyl transferase (MGMT) activity ...

    Myeloperoxidase (MPO) generates reactive oxygen species that potentially contribute to many chronic inflammatory diseases. A recently reported triazolopyrimidine MPO inhibitor was optimized to improve acid stability and remove methyl guanine methyl transferase (MGMT) activity. Multiple synthetic routes were explored that allowed rapid optimization of a key benzyl ether side chain. Crystal structures of inhibitors bound to the MPO active site demonstrated alternate binding modes and guided rational design of MPO inhibitors. Thioether 36 showed significant inhibition of MPO activity in an acute mouse inflammation model after oral dosing.


    Organizational Affiliation

    Bristol-Myers Squibb Research and Development, P.O. Box 5400, Princeton, New Jersey 08534, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyeloperoxidaseA, C [auth D], E [auth F], G [auth H]105Homo sapiensMutation(s): 0 
Gene Names: MPO
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MyeloperoxidaseB, D [auth E], F [auth G], H [auth I]467Homo sapiensMutation(s): 0 
Gene Names: MPO
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
FA [auth E], FB [auth I], OA [auth G], P [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
JXS (Subject of Investigation/LOI)
Query on JXS

Download Ideal Coordinates CCD File 
GA [auth E], TA [auth G], U [auth B]7-{[3-(1-methyl-1H-pyrazol-3-yl)phenyl]methoxy}-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
C16 H15 N7 O
WGMJNFFLMIILAZ-UHFFFAOYSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth E] , AB [auth I] , BA [auth E] , BB [auth I] , CA [auth E] , CB [auth I] , DA [auth E] , DB [auth I] , 
AA [auth E], AB [auth I], BA [auth E], BB [auth I], CA [auth E], CB [auth I], DA [auth E], DB [auth I], I [auth B], IA [auth G], J [auth B], JA [auth G], K [auth B], KA [auth G], L [auth B], LA [auth G], M [auth B], NA [auth G], O [auth B], PA [auth G], Q [auth B], WA [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
RA [auth G], S [auth B], SA [auth G], T [auth B], Y [auth E], YA [auth I], Z [auth E], ZA [auth I]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA (Subject of Investigation/LOI)
Query on BMA

Download Ideal Coordinates CCD File 
QA [auth G], R [auth B], X [auth E], XA [auth I]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
FUC (Subject of Investigation/LOI)
Query on FUC

Download Ideal Coordinates CCD File 
EA [auth E], EB [auth I], MA [auth G], N [auth B]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
GB [auth I], HA [auth E], UA [auth G], V [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
VA [auth G], W [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.817α = 90
b = 150.949β = 90
c = 233.104γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-09-26 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Khan, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2021-05-12
    Changes: Structure summary