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Iron in PDB 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

Enzymatic activity of 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

All present enzymatic activity of 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:
1.11.2.2;

Protein crystallography data

The structure of 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, PDB code: 5qj2 was solved by J.A.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 116.55 / 2.82
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 143.817, 150.949, 233.104, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 27.2

Other elements in 5qj2:

The structure of 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 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the 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 (pdb code 5qj2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 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, PDB code: 5qj2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5qj2

Go back to Iron Binding Sites List in 5qj2
Iron binding site 1 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe608

b:50.2
occ:1.00
 FE B:HEM608 0.0 50.2 1.0
NB B:HEM608 1.9 49.9 1.0
NC B:HEM608 1.9 50.1 1.0
NA B:HEM608 1.9 50.4 1.0
ND B:HEM608 2.0 50.2 1.0
NE2 B:HIS336 2.1 49.8 1.0
C4B B:HEM608 2.9 50.2 1.0
C1C B:HEM608 2.9 50.0 1.0
C4C B:HEM608 2.9 50.3 1.0
C1B B:HEM608 2.9 50.3 1.0
C4D B:HEM608 3.0 50.5 1.0
C1D B:HEM608 3.0 50.6 1.0
C4A B:HEM608 3.0 50.3 1.0
C1A B:HEM608 3.0 50.5 1.0
CD2 B:HIS336 3.1 50.0 1.0
CE1 B:HIS336 3.2 49.5 1.0
CHC B:HEM608 3.3 50.7 1.0
CHB B:HEM608 3.4 50.8 1.0
CHD B:HEM608 3.4 51.0 1.0
N21 B:JXS613 3.4 75.6 1.0
CHA B:HEM608 3.4 50.9 1.0
N20 B:JXS613 3.5 77.0 1.0
C2C B:HEM608 4.1 50.6 1.0
C3B B:HEM608 4.1 50.7 1.0
C3C B:HEM608 4.1 50.7 1.0
C2B B:HEM608 4.1 50.4 1.0
C2A B:HEM608 4.2 50.9 1.0
CG B:HIS336 4.2 48.4 1.0
C3A B:HEM608 4.2 50.9 1.0
C3D B:HEM608 4.2 51.0 1.0
C2D B:HEM608 4.2 51.0 1.0
ND1 B:HIS336 4.3 50.1 1.0
C13 B:JXS613 4.3 75.3 1.0
N17 B:JXS613 4.4 76.0 1.0
C10 B:JXS613 4.8 74.7 1.0
CD2 B:LEU417 4.9 49.6 1.0
NE2 A:GLN91 4.9 61.9 1.0

Iron binding site 2 out of 4 in 5qj2

Go back to Iron Binding Sites List in 5qj2
Iron binding site 2 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe609

b:59.7
occ:1.00
 FE E:HEM609 0.0 59.7 1.0
NA E:HEM609 1.9 59.9 1.0
NB E:HEM609 1.9 59.5 1.0
ND E:HEM609 2.0 59.8 1.0
NC E:HEM609 2.0 59.6 1.0
NE2 E:HIS336 2.0 44.5 1.0
C1B E:HEM609 2.9 59.9 1.0
C4B E:HEM609 3.0 59.7 1.0
C1D E:HEM609 3.0 60.1 1.0
C4A E:HEM609 3.0 59.9 1.0
C4D E:HEM609 3.0 60.1 1.0
C4C E:HEM609 3.0 59.8 1.0
C1A E:HEM609 3.0 60.1 1.0
C1C E:HEM609 3.0 59.5 1.0
CE1 E:HIS336 3.0 44.7 1.0
CD2 E:HIS336 3.0 45.1 1.0
CHB E:HEM609 3.3 60.3 1.0
CHD E:HEM609 3.4 60.6 1.0
CHA E:HEM609 3.4 60.5 1.0
CHC E:HEM609 3.4 60.2 1.0
N21 E:JXS610 3.7 70.5 1.0
N20 E:JXS610 3.9 71.6 1.0
CG E:HIS336 4.2 44.9 1.0
C2B E:HEM609 4.2 60.0 1.0
ND1 E:HIS336 4.2 46.0 1.0
C3A E:HEM609 4.2 60.5 1.0
C3B E:HEM609 4.2 60.2 1.0
C2A E:HEM609 4.2 60.5 1.0
C2C E:HEM609 4.2 60.1 1.0
C3C E:HEM609 4.2 60.2 1.0
C2D E:HEM609 4.3 60.6 1.0
C3D E:HEM609 4.3 60.7 1.0
C13 E:JXS610 4.5 70.7 1.0
CD2 E:LEU417 4.7 48.9 1.0
NE2 D:GLN91 4.7 28.8 1.0
N17 E:JXS610 4.7 70.2 1.0
CG E:ARG333 4.9 44.6 1.0

Iron binding site 3 out of 4 in 5qj2

Go back to Iron Binding Sites List in 5qj2
Iron binding site 3 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe607

b:45.1
occ:1.00
 FE G:HEM607 0.0 45.1 1.0
NB G:HEM607 1.9 44.8 1.0
NA G:HEM607 2.0 45.3 1.0
NC G:HEM607 2.0 45.1 1.0
ND G:HEM607 2.0 45.2 1.0
NE2 G:HIS336 2.1 47.9 1.0
C4B G:HEM607 2.9 45.1 1.0
C1B G:HEM607 2.9 45.2 1.0
C4D G:HEM607 3.0 45.6 1.0
C4A G:HEM607 3.0 45.2 1.0
C1D G:HEM607 3.0 45.6 1.0
C4C G:HEM607 3.0 45.3 1.0
C1C G:HEM607 3.0 45.0 1.0
C1A G:HEM607 3.1 45.5 1.0
CE1 G:HIS336 3.1 47.8 1.0
CD2 G:HIS336 3.2 48.3 1.0
CHB G:HEM607 3.4 45.6 1.0
CHC G:HEM607 3.4 45.7 1.0
CHA G:HEM607 3.4 45.9 1.0
CHD G:HEM607 3.4 46.0 1.0
N21 G:JXS612 3.6 54.1 1.0
N20 G:JXS612 3.9 55.8 1.0
C3B G:HEM607 4.2 45.6 1.0
C2B G:HEM607 4.2 45.3 1.0
C3A G:HEM607 4.2 45.8 1.0
C3C G:HEM607 4.3 45.6 1.0
C2C G:HEM607 4.3 45.6 1.0
C2A G:HEM607 4.3 45.9 1.0
ND1 G:HIS336 4.3 48.5 1.0
C3D G:HEM607 4.3 46.0 1.0
CG G:HIS336 4.3 46.6 1.0
C2D G:HEM607 4.3 46.0 1.0
C13 G:JXS612 4.3 54.6 1.0
N17 G:JXS612 4.7 53.3 1.0
CD2 G:LEU417 4.8 44.5 1.0
C10 G:JXS612 4.9 54.7 1.0

Iron binding site 4 out of 4 in 5qj2

Go back to Iron Binding Sites List in 5qj2
Iron binding site 4 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe610

b:45.6
occ:1.00
 FE I:HEM610 0.0 45.6 1.0
NC I:HEM610 1.9 45.4 1.0
NB I:HEM610 2.0 45.4 1.0
NA I:HEM610 2.0 45.8 1.0
ND I:HEM610 2.0 45.7 1.0
NE2 I:HIS336 2.1 52.9 1.0
C4C I:HEM610 3.0 45.7 1.0
C1B I:HEM610 3.0 45.7 1.0
C1C I:HEM610 3.0 45.4 1.0
C4B I:HEM610 3.0 45.6 1.0
C4D I:HEM610 3.0 46.0 1.0
C4A I:HEM610 3.0 45.8 1.0
C1D I:HEM610 3.0 46.0 1.0
C1A I:HEM610 3.1 45.9 1.0
CE1 I:HIS336 3.1 52.9 1.0
CD2 I:HIS336 3.1 53.1 1.0
CHD I:HEM610 3.4 46.4 1.0
CHB I:HEM610 3.4 46.2 1.0
CHC I:HEM610 3.4 46.1 1.0
CHA I:HEM610 3.4 46.4 1.0
C2C I:HEM610 4.1 45.9 1.0
C3C I:HEM610 4.1 46.0 1.0
C2B I:HEM610 4.2 45.9 1.0
C3B I:HEM610 4.2 46.1 1.0
CG I:HIS336 4.2 52.1 1.0
ND1 I:HIS336 4.2 53.8 1.0
C3A I:HEM610 4.2 46.3 1.0
C2A I:HEM610 4.3 46.3 1.0
C3D I:HEM610 4.3 46.5 1.0
C2D I:HEM610 4.3 46.4 1.0
CD2 I:LEU417 4.9 45.3 1.0
CG I:ARG333 4.9 39.1 1.0
NE2 H:GLN91 5.0 39.5 1.0

Reference:

N.R.Wurtz, A.Viet, S.A.Shaw, A.Dilger, M.N.Valente, J.A.Khan, S.Jusuf, R.Narayanan, G.Fernando, F.Lo, X.Liu, G.A.Locke, L.Kopcho, L.M.Abell, P.Sleph, M.Basso, L.Zhao, R.R.Wexler, F.Duclos, E.K.Kick. Potent Triazolopyridine Myeloperoxidase Inhibitors. Acs Med Chem Lett V. 9 1175 2018.
ISSN: ISSN 1948-5875
PubMed: 30613322
DOI: 10.1021/ACSMEDCHEMLETT.8B00308
Page generated: Tue Aug 6 08:32:10 2024

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