6WYD

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myeloperoxidase light chainA, 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Myeloperoxidase heavy chainB, 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
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
FA [auth E], IB [auth I], O [auth B], PA [auth G]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
7GD (Subject of Investigation/LOI)
Query on 7GD

Download Ideal Coordinates CCD File 
GA [auth E], T [auth B], UA [auth G], XA [auth H]7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
C12 H11 N5
SGFFXIGIHATQNC-UHFFFAOYSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth E] , CA [auth E] , DA [auth E] , DB [auth I] , EB [auth I] , FB [auth I] , GB [auth I] , 
AA [auth E], BA [auth E], CA [auth E], DA [auth E], DB [auth I], EB [auth I], FB [auth I], GB [auth I], J [auth B], K [auth B], L [auth B], LA [auth G], M [auth B], MA [auth G], NA [auth G], P [auth B], QA [auth G], W [auth E], ZA [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 
BB [auth I], CB [auth I], R [auth B], S [auth B], SA [auth G], TA [auth G], Y [auth E], Z [auth E]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA (Subject of Investigation/LOI)
Query on BMA

Download Ideal Coordinates CCD File 
AB [auth I], Q [auth B], RA [auth G], X [auth E]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], HB [auth I], N [auth B], OA [auth G]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CA
Query on CA

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

Download Ideal Coordinates CCD File 
I [auth A], IA [auth E], JA [auth E], KA [auth F], KB [auth I], V [auth B], WA [auth G], YA [auth H]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.683α = 90
b = 150.651β = 90
c = 231.06γ = 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

  • Deposited Date: 2020-05-12 
  • 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