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Calcium in PDB 7lag: Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine

Enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine

All present enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[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) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine, PDB code: 7lag 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) 47.20 / 2.81
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 143.459, 149.886, 228.642, 90, 90, 90
R / Rfree (%) 19.3 / 23.5

Other elements in 7lag:

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine (pdb code 7lag). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine, PDB code: 7lag:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7lag

Go back to Calcium Binding Sites List in 7lag
Calcium binding site 1 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca611

b:36.1
occ:1.00
 O A:ASP96 2.1 34.6 1.0
O B:PHE170 2.2 37.7 1.0
O B:THR168 2.4 39.6 1.0
OD1 B:ASP172 2.4 36.5 1.0
OD1 A:ASP96 2.5 47.2 1.0
OG B:SER174 2.5 39.9 1.0
OG1 B:THR168 2.5 39.1 1.0
C A:ASP96 3.2 36.4 1.0
C B:THR168 3.4 39.3 1.0
CG B:ASP172 3.4 38.2 1.0
C B:PHE170 3.4 39.0 1.0
CB B:SER174 3.6 36.7 1.0
CG A:ASP96 3.6 47.3 1.0
OD2 B:ASP172 3.8 43.9 1.0
CB B:THR168 3.8 38.3 1.0
N B:PHE170 3.9 36.6 1.0
CA A:ASP96 4.0 32.7 1.0
CA B:THR168 4.0 35.3 1.0
C B:SER169 4.1 42.1 1.0
N B:ASP172 4.1 33.0 1.0
CA B:PHE170 4.1 35.1 1.0
CB A:ASP96 4.2 35.0 1.0
N B:THR168 4.3 35.3 1.0
N A:LEU97 4.3 33.2 1.0
N B:SER174 4.3 36.9 1.0
N B:SER169 4.3 36.5 1.0
O B:SER169 4.3 42.7 1.0
N B:VAL171 4.5 36.4 1.0
CA B:SER174 4.5 36.4 1.0
CA A:LEU97 4.6 31.3 1.0
CB B:ASP172 4.6 32.7 1.0
CA B:SER169 4.6 37.3 1.0
OD2 A:ASP96 4.6 54.7 1.0
CB B:PHE170 4.7 35.9 1.0
CA B:VAL171 4.8 35.3 1.0
CA B:ASP172 4.8 32.0 1.0
CG2 B:THR168 4.9 30.1 1.0
C B:VAL171 5.0 37.9 1.0
N B:ALA173 5.0 35.4 1.0

Calcium binding site 2 out of 4 in 7lag

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Calcium binding site 2 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca610

b:32.5
occ:1.00
 O D:ASP96 2.1 38.6 1.0
O E:PHE170 2.2 30.1 1.0
OD1 E:ASP172 2.4 34.3 1.0
OD1 D:ASP96 2.4 44.6 1.0
OG E:SER174 2.5 35.3 1.0
O E:THR168 2.5 35.1 1.0
OG1 E:THR168 2.6 44.8 1.0
C D:ASP96 3.2 37.1 1.0
CG E:ASP172 3.3 35.3 1.0
C E:PHE170 3.4 32.5 1.0
C E:THR168 3.4 37.3 1.0
CB E:SER174 3.5 30.3 1.0
CG D:ASP96 3.5 44.4 1.0
OD2 E:ASP172 3.7 32.8 1.0
CB E:THR168 3.8 39.1 1.0
N E:PHE170 3.9 30.9 1.0
CA D:ASP96 3.9 32.4 1.0
N E:ASP172 4.1 33.1 1.0
CA E:THR168 4.1 34.6 1.0
C E:SER169 4.1 37.5 1.0
CA E:PHE170 4.1 30.5 1.0
CB D:ASP96 4.2 34.0 1.0
N E:SER174 4.2 31.2 1.0
N D:LEU97 4.3 32.1 1.0
N E:THR168 4.3 34.6 1.0
N E:SER169 4.4 34.2 1.0
O E:SER169 4.4 39.2 1.0
N E:VAL171 4.4 29.9 1.0
CA E:SER174 4.5 30.0 1.0
OD2 D:ASP96 4.5 51.3 1.0
CB E:ASP172 4.5 33.9 1.0
CA D:LEU97 4.6 30.8 1.0
CA E:SER169 4.6 33.1 1.0
CB E:PHE170 4.7 32.8 1.0
CA E:VAL171 4.7 30.3 1.0
CA E:ASP172 4.8 32.9 1.0
CG2 E:THR168 4.9 32.7 1.0
C E:VAL171 4.9 36.9 1.0
N E:ALA173 4.9 35.3 1.0

Calcium binding site 3 out of 4 in 7lag

Go back to Calcium Binding Sites List in 7lag
Calcium binding site 3 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca611

b:35.0
occ:1.00
 O F:ASP96 2.1 36.3 1.0
O G:PHE170 2.3 27.9 1.0
O G:THR168 2.3 36.6 1.0
OG G:SER174 2.4 39.4 1.0
OG1 G:THR168 2.5 37.4 1.0
OD1 G:ASP172 2.5 33.9 1.0
OD1 F:ASP96 2.7 49.0 1.0
C G:THR168 3.3 36.4 1.0
C F:ASP96 3.3 36.4 1.0
CG G:ASP172 3.4 28.8 1.0
C G:PHE170 3.4 28.9 1.0
CB G:SER174 3.5 31.0 1.0
CB G:THR168 3.7 35.1 1.0
CG F:ASP96 3.8 47.0 1.0
OD2 G:ASP172 3.8 29.3 1.0
N G:PHE170 3.9 27.8 1.0
CA G:THR168 3.9 32.7 1.0
CA F:ASP96 4.0 31.6 1.0
C G:SER169 4.0 35.5 1.0
CA G:PHE170 4.1 25.1 1.0
N G:THR168 4.2 32.9 1.0
N G:ASP172 4.2 23.3 1.0
N G:SER169 4.2 32.5 1.0
CB F:ASP96 4.3 32.5 1.0
N G:SER174 4.3 29.0 1.0
O G:SER169 4.3 37.5 1.0
N F:LEU97 4.4 31.6 1.0
N G:VAL171 4.5 27.5 1.0
CA G:SER174 4.5 29.9 1.0
CA G:SER169 4.5 31.8 1.0
CA F:LEU97 4.6 30.1 1.0
CB G:ASP172 4.7 20.9 1.0
CB G:PHE170 4.7 26.2 1.0
OD2 F:ASP96 4.7 54.5 1.0
CA G:VAL171 4.8 27.3 1.0
CG2 G:THR168 4.8 23.2 1.0
CA G:ASP172 4.9 21.5 1.0

Calcium binding site 4 out of 4 in 7lag

Go back to Calcium Binding Sites List in 7lag
Calcium binding site 4 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-14 Aka 7-({1-[(3-Phenoxyphenyl)Methyl]-1H-Pyrazol-4- Yl}Methyl)-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca610

b:32.8
occ:1.00
 O H:ASP96 2.1 30.6 1.0
OG I:SER174 2.3 33.5 1.0
O I:THR168 2.4 36.7 1.0
O I:PHE170 2.4 33.1 1.0
OG1 I:THR168 2.4 30.8 1.0
OD1 I:ASP172 2.5 24.4 1.0
OD1 H:ASP96 2.6 47.3 1.0
C H:ASP96 3.2 34.9 1.0
C I:THR168 3.3 35.9 1.0
CB I:SER174 3.4 33.4 1.0
CG I:ASP172 3.4 28.3 1.0
C I:PHE170 3.6 32.5 1.0
CB I:THR168 3.7 29.7 1.0
CG H:ASP96 3.7 46.5 1.0
OD2 I:ASP172 3.8 33.4 1.0
CA I:THR168 3.9 31.9 1.0
CA H:ASP96 4.0 33.7 1.0
N I:PHE170 4.0 31.1 1.0
N I:THR168 4.2 33.3 1.0
C I:SER169 4.2 36.5 1.0
N I:SER174 4.2 33.0 1.0
N I:ASP172 4.3 25.3 1.0
CA I:PHE170 4.3 29.7 1.0
CB H:ASP96 4.3 35.8 1.0
N H:LEU97 4.3 34.8 1.0
N I:SER169 4.3 32.3 1.0
CA I:SER174 4.4 33.1 1.0
O I:SER169 4.5 37.3 1.0
CA H:LEU97 4.6 35.0 1.0
N I:VAL171 4.6 27.3 1.0
CA I:SER169 4.7 32.4 1.0
CB I:ASP172 4.7 24.8 1.0
OD2 H:ASP96 4.7 55.1 1.0
CG2 I:THR168 4.8 17.6 1.0
CB I:PHE170 4.8 31.4 1.0
CA I:ASP172 4.9 25.0 1.0
CA I:VAL171 4.9 26.0 1.0

Reference:

C.H.Hu, M.W.Neissel Valente, O.Scott Halpern, S.Jusuf, J.A.Khan, G.A.Locke, G.J.Duke, X.Liu, F.J.Duclos, R.R.Wexler, E.K.Kick, J.M.Smallheer. Small Molecule and Macrocyclic Pyrazole Derived Inhibitors of Myeloperoxidase (Mpo). Bioorg.Med.Chem.Lett. 28010 2021.
ISSN: ESSN 1464-3405
PubMed: 33811992
DOI: 10.1016/J.BMCL.2021.128010
Page generated: Fri Jul 19 01:34:59 2024

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