5WDJ

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-6 AKA 7-(BENZYLOXY)-1H-[1,2, 3]TRIAZOLO[4,5-D]PYRIMIDIN-5-AMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Triazolopyrimidines identified as reversible myeloperoxidase inhibitors.

Duclos, F.Abell, L.M.Harden, D.G.Pike, K.Nowak, K.Locke, G.A.Duke, G.J.Liu, X.Fernando, G.Shaw, S.A.Vokits, B.P.Wurtz, N.R.Viet, A.Valente, M.N.Stachura, S.Sleph, P.Khan, J.A.Gao, J.Dongre, A.R.Zhao, L.Wexler, R.R.Gordon, D.A.Kick, E.K.

(2017) Medchemcomm 8: 2093-2099


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myeloperoxidase
A, D
105Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.2.2
Find proteins for P05164 (Homo sapiens)
Go to Gene View: MPO
Go to UniProtKB:  P05164
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Myeloperoxidase
B, E
467Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.2.2
Find proteins for P05164 (Homo sapiens)
Go to Gene View: MPO
Go to UniProtKB:  P05164
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AEY
Query on AEY

Download SDF File 
Download CCD File 
A, E
7-(benzyloxy)-1H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine
C11 H10 N6 O
ZHTBAYPUCDCQPX-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, D, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, E
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B, E
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.925α = 90.00
b = 103.925β = 90.00
c = 242.276γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-07-05 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Khan, J.A.

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references