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Calcium in PDB 6wy0: Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5- Amine

Enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5- Amine, PDB code: 6wy0 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) 47.69 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 145.348, 151.402, 229.728, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.6

Other elements in 6wy0:

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5- Amine also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5- Amine (pdb code 6wy0). 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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5- Amine, PDB code: 6wy0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6wy0

Go back to Calcium Binding Sites List in 6wy0
Calcium binding site 1 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-3H-[1,2,3]Triazolo[4,5-B]Pyridin-5- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca609

b:50.7
occ:1.00
 O A:ASP96 2.1 51.8 1.0
O B:THR168 2.3 49.4 1.0
OG1 B:THR168 2.4 50.2 1.0
OD1 B:ASP172 2.5 59.9 1.0
OD1 A:ASP96 2.5 61.4 1.0
O B:PHE170 2.6 49.7 1.0
OG B:SER174 2.6 59.8 1.0
CB B:SER174 3.1 57.8 1.0
C B:THR168 3.3 48.8 1.0
C A:ASP96 3.3 51.4 1.0
CG B:ASP172 3.5 60.1 1.0
CB B:THR168 3.6 49.2 1.0
CG A:ASP96 3.6 59.8 1.0
C B:PHE170 3.7 50.4 1.0
OD2 B:ASP172 3.8 63.4 1.0
CA B:THR168 3.8 48.2 1.0
CA A:ASP96 4.0 52.3 1.0
N B:THR168 4.0 47.8 1.0
N B:PHE170 4.1 48.9 1.0
N B:SER174 4.1 56.2 1.0
CA B:SER174 4.2 56.6 1.0
C B:SER169 4.3 49.4 1.0
CB A:ASP96 4.3 54.5 1.0
N B:ASP172 4.3 54.3 1.0
N B:SER169 4.3 48.7 1.0
N A:LEU97 4.4 49.6 1.0
CA B:PHE170 4.4 49.5 1.0
OD2 A:ASP96 4.6 61.6 1.0
CG2 B:THR168 4.6 49.2 1.0
O B:SER169 4.7 50.2 1.0
CA B:SER169 4.7 49.0 1.0
CA A:LEU97 4.7 47.9 1.0
CB B:ASP172 4.7 56.3 1.0
N B:VAL171 4.8 51.1 1.0
OG B:SER179 4.9 65.1 1.0
CB B:PHE170 5.0 49.0 1.0
CB B:LEU167 5.0 46.7 1.0
CA B:ASP172 5.0 54.9 1.0

Calcium binding site 2 out of 4 in 6wy0

Go back to Calcium Binding Sites List in 6wy0
Calcium binding site 2 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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:41.5
occ:1.00
 O D:ASP96 2.2 41.7 1.0
O E:PHE170 2.3 39.8 1.0
OD1 E:ASP172 2.3 49.3 1.0
OD1 D:ASP96 2.4 48.4 1.0
O E:THR168 2.4 40.0 1.0
OG1 E:THR168 2.5 43.5 1.0
OG E:SER174 2.7 51.1 1.0
CB E:SER174 3.3 47.8 1.0
CG E:ASP172 3.4 47.7 1.0
C D:ASP96 3.4 40.9 1.0
C E:THR168 3.4 39.1 1.0
C E:PHE170 3.4 40.5 1.0
CG D:ASP96 3.6 47.1 1.0
CB E:THR168 3.8 41.1 1.0
OD2 E:ASP172 3.8 48.4 1.0
N E:PHE170 3.9 39.6 1.0
CA D:ASP96 4.0 41.2 1.0
CA E:THR168 4.1 38.3 1.0
N E:ASP172 4.1 42.6 1.0
N E:SER174 4.1 47.0 1.0
CA E:PHE170 4.2 39.7 1.0
C E:SER169 4.2 39.7 1.0
N E:THR168 4.3 36.8 1.0
CB D:ASP96 4.3 43.2 1.0
CA E:SER174 4.3 46.7 1.0
N E:SER169 4.4 38.8 1.0
N D:LEU97 4.5 40.1 1.0
OD2 D:ASP96 4.5 47.5 1.0
N E:VAL171 4.5 41.3 1.0
O E:SER169 4.6 40.4 1.0
CB E:ASP172 4.6 43.9 1.0
CA E:SER169 4.7 39.1 1.0
CA E:VAL171 4.7 41.9 1.0
CB E:PHE170 4.8 39.2 1.0
CA D:LEU97 4.8 39.7 1.0
CA E:ASP172 4.8 43.7 1.0
CG2 E:THR168 4.8 41.2 1.0
C E:VAL171 5.0 42.2 1.0

Calcium binding site 3 out of 4 in 6wy0

Go back to Calcium Binding Sites List in 6wy0
Calcium binding site 3 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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:34.1
occ:1.00
 OG G:SER174 2.2 42.8 1.0
O F:ASP96 2.3 39.4 1.0
O G:THR168 2.3 37.9 1.0
OD1 G:ASP172 2.4 43.8 1.0
OG1 G:THR168 2.4 42.6 1.0
O G:PHE170 2.5 38.0 1.0
OD1 F:ASP96 2.5 44.2 1.0
C G:THR168 3.3 37.9 1.0
CB G:SER174 3.4 40.8 1.0
CG G:ASP172 3.4 43.1 1.0
C F:ASP96 3.4 39.5 1.0
C G:PHE170 3.6 37.9 1.0
CB G:THR168 3.7 40.2 1.0
CG F:ASP96 3.7 44.3 1.0
OD2 G:ASP172 3.8 45.4 1.0
CA G:THR168 3.9 37.7 1.0
N G:PHE170 4.0 37.4 1.0
CA F:ASP96 4.1 39.7 1.0
N G:THR168 4.1 36.6 1.0
N G:SER174 4.1 39.6 1.0
N G:ASP172 4.2 38.6 1.0
C G:SER169 4.2 38.1 1.0
CA G:SER174 4.3 39.9 1.0
CA G:PHE170 4.3 37.1 1.0
N G:SER169 4.4 38.0 1.0
CB F:ASP96 4.4 40.7 1.0
N F:LEU97 4.5 39.7 1.0
OD2 F:ASP96 4.6 45.6 1.0
O G:SER169 4.6 38.9 1.0
CB G:ASP172 4.7 39.0 1.0
CG2 G:THR168 4.7 40.3 1.0
CA G:SER169 4.7 37.9 1.0
N G:VAL171 4.7 38.1 1.0
CB G:PHE170 4.8 36.2 1.0
CA F:LEU97 4.9 40.1 1.0
CA G:ASP172 4.9 38.8 1.0
CA G:VAL171 4.9 38.3 1.0

Calcium binding site 4 out of 4 in 6wy0

Go back to Calcium Binding Sites List in 6wy0
Calcium binding site 4 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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-40 A.K.A 7-[(1R)-1-Phenyl-3-{[(1R,4R)-4- Phenylcyclohexyl]Amino}Propyl]-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:41.1
occ:1.00
 O H:ASP96 2.2 44.2 1.0
OD1 H:ASP96 2.2 53.5 1.0
O I:THR168 2.4 40.6 1.0
OD1 I:ASP172 2.5 48.0 1.0
OG I:SER174 2.5 47.9 1.0
O I:PHE170 2.6 44.7 1.0
OG1 I:THR168 2.6 42.1 1.0
CB I:SER174 3.1 46.0 1.0
C H:ASP96 3.3 44.6 1.0
CG H:ASP96 3.4 52.1 1.0
C I:THR168 3.5 40.4 1.0
CG I:ASP172 3.5 47.9 1.0
C I:PHE170 3.8 44.9 1.0
CB I:THR168 3.8 41.3 1.0
CA H:ASP96 3.9 45.4 1.0
OD2 I:ASP172 4.0 50.5 1.0
N I:SER174 4.0 45.7 1.0
CA I:THR168 4.0 39.8 1.0
CA I:SER174 4.1 45.6 1.0
CB H:ASP96 4.1 47.4 1.0
N I:THR168 4.2 39.1 1.0
N I:PHE170 4.2 43.6 1.0
N I:ASP172 4.3 45.2 1.0
OD2 H:ASP96 4.3 53.8 1.0
N H:LEU97 4.4 44.4 1.0
C I:SER169 4.4 43.6 1.0
CA I:PHE170 4.5 43.9 1.0
N I:SER169 4.5 41.1 1.0
CB I:ASP172 4.8 45.1 1.0
N I:VAL171 4.8 45.4 1.0
CA H:LEU97 4.8 44.9 1.0
CG2 I:THR168 4.8 41.6 1.0
O I:SER169 4.8 44.1 1.0
CA I:SER169 4.8 42.7 1.0
CA I:VAL171 4.9 46.1 1.0
CA I:ASP172 4.9 44.9 1.0

Reference:

S.A.Shaw, B.P.Vokits, A.K.Dilger, A.Viet, C.G.Clark, L.M.Abell, G.A.Locke, G.Duke, L.M.Kopcho, A.Dongre, J.Gao, A.Krishnakumar, S.Jusuf, J.Khan, S.A.Spronk, M.D.Basso, L.Zhao, G.H.Cantor, J.M.Onorato, R.R.Wexler, F.Duclos, E.K.Kick. Discovery and Structure Activity Relationships of 7-Benzyl Triazolopyridines As Stable, Selective, and Reversible Inhibitors of Myeloperoxidase. Bioorg.Med.Chem. V. 28 15723 2020.
ISSN: ESSN 1464-3391
PubMed: 33007547
DOI: 10.1016/J.BMC.2020.115723
Page generated: Tue Jul 16 17:34:45 2024

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