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Chlorine in PDB 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

Enzymatic activity of 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

All present enzymatic activity of 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:
1.11.2.2;

Protein crystallography data

The structure of 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, PDB code: 5wdj 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) 95.51 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.925, 103.925, 242.276, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.8

Other elements in 5wdj:

The structure of 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 also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 5wdj

Go back to Chlorine Binding Sites List in 5wdj
Chlorine binding site 1 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:29.0
occ:1.00
 N B:VAL327 3.1 18.3 1.0
O A:HOH339 3.2 19.2 1.0
N A:TRP32 3.3 19.9 1.0
CB B:ASN326 3.6 17.7 1.0
N B:ASN326 3.6 17.9 1.0
CH2 B:TRP436 3.6 17.3 1.0
CB B:VAL327 3.6 18.5 1.0
CG1 B:VAL327 3.6 17.5 1.0
CA A:ARG31 3.8 19.7 1.0
CA B:ASN326 3.8 18.1 1.0
C B:ASN326 3.9 18.2 1.0
CA B:VAL327 3.9 18.4 1.0
CZ2 B:TRP436 4.0 17.5 1.0
C A:ARG31 4.0 19.8 1.0
CD2 B:LEU430 4.1 18.2 1.0
O A:VAL30 4.1 19.0 1.0
C B:ALA325 4.3 17.5 1.0
CB A:TRP32 4.3 19.6 1.0
CG A:ARG31 4.3 20.2 1.0
CA A:TRP32 4.3 19.8 1.0
CB A:ARG31 4.3 20.0 1.0
CB B:ALA325 4.3 17.3 1.0
N A:LEU33 4.4 20.4 1.0
CA B:ALA325 4.7 17.3 1.0
NH1 A:ARG31 4.7 20.4 1.0
CZ3 B:TRP436 4.8 17.6 1.0
CG A:TRP32 4.8 18.5 1.0
O A:LEU33 4.8 20.6 1.0
CG B:ASN326 4.8 18.2 1.0
C A:TRP32 4.9 20.1 1.0
N A:ARG31 4.9 19.2 1.0
C A:VAL30 4.9 19.1 1.0
O B:ALA325 5.0 17.2 1.0

Chlorine binding site 2 out of 4 in 5wdj

Go back to Chlorine Binding Sites List in 5wdj
Chlorine binding site 2 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:47.0
occ:1.00
 N B:PHE213 3.8 25.7 1.0
N B:GLN201 3.8 23.4 1.0
OD1 B:ASN200 3.9 22.4 1.0
CG B:ASN200 4.1 22.3 1.0
CD2 B:PHE213 4.2 26.3 1.0
ND2 B:ASN200 4.3 22.0 1.0
CB B:PHE213 4.3 26.3 1.0
CA B:ASN200 4.4 22.6 1.0
CA B:PRO212 4.5 24.4 1.0
CB B:GLN201 4.5 24.1 1.0
CG B:ARG202 4.5 26.4 1.0
CG B:PHE213 4.6 26.4 1.0
CA B:PHE213 4.6 26.5 1.0
CA B:GLN201 4.6 24.0 1.0
C B:PRO212 4.6 24.9 1.0
C B:ASN200 4.6 23.0 1.0
N B:ARG202 4.6 24.8 1.0
CB B:PRO212 4.8 24.3 1.0
CG B:GLN201 4.8 24.5 1.0
O B:PHE213 4.9 26.9 1.0
CB B:ASN200 4.9 22.5 1.0

Chlorine binding site 3 out of 4 in 5wdj

Go back to Chlorine Binding Sites List in 5wdj
Chlorine binding site 3 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:26.1
occ:1.00
 N E:VAL327 3.2 17.8 1.0
N D:TRP32 3.3 19.2 1.0
O D:HOH338 3.3 14.7 1.0
CB E:ASN326 3.5 17.1 1.0
CA D:ARG31 3.6 19.2 1.0
N E:ASN326 3.6 17.4 1.0
CG1 E:VAL327 3.7 17.2 1.0
CH2 E:TRP436 3.8 16.7 1.0
CB E:VAL327 3.8 17.7 1.0
CA E:ASN326 3.9 17.6 1.0
C D:ARG31 4.0 19.2 1.0
O D:VAL30 4.0 18.9 1.0
C E:ASN326 4.0 17.8 1.0
CG D:ARG31 4.1 19.8 1.0
CZ2 E:TRP436 4.1 17.4 1.0
CA E:VAL327 4.1 18.0 1.0
CB D:ARG31 4.1 19.2 1.0
CD2 E:LEU430 4.2 16.4 1.0
CA D:TRP32 4.3 19.3 1.0
N D:LEU33 4.3 19.5 1.0
CB D:TRP32 4.3 18.9 1.0
C E:ALA325 4.3 17.3 1.0
CB E:ALA325 4.4 16.9 1.0
N D:ARG31 4.7 19.1 1.0
O D:LEU33 4.7 20.2 1.0
NH1 D:ARG31 4.7 19.8 1.0
CA E:ALA325 4.8 17.4 1.0
CG E:ASN326 4.8 17.6 1.0
C D:VAL30 4.8 18.9 1.0
C D:TRP32 4.8 19.3 1.0
CG D:TRP32 4.8 18.4 1.0
CD D:ARG31 4.9 20.9 1.0
CZ3 E:TRP436 4.9 17.4 1.0

Chlorine binding site 4 out of 4 in 5wdj

Go back to Chlorine Binding Sites List in 5wdj
Chlorine binding site 4 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl612

b:45.2
occ:1.00
 N E:GLN201 3.7 23.5 1.0
OD1 E:ASN200 3.8 21.8 1.0
N E:PHE213 3.9 25.2 1.0
CG E:ASN200 4.1 22.4 1.0
CG E:ARG202 4.2 26.5 1.0
CA E:ASN200 4.3 22.7 1.0
CD2 E:PHE213 4.3 26.6 1.0
CB E:PHE213 4.3 26.3 1.0
ND2 E:ASN200 4.4 22.6 1.0
CB E:GLN201 4.4 24.0 1.0
C E:ASN200 4.5 23.2 1.0
CA E:PRO212 4.6 23.9 1.0
CA E:GLN201 4.6 24.1 1.0
CG E:GLN201 4.6 24.1 1.0
N E:ARG202 4.6 24.7 1.0
CA E:PHE213 4.7 26.3 1.0
CG E:PHE213 4.7 26.6 1.0
CB E:PRO212 4.8 23.8 1.0
C E:PRO212 4.8 24.4 1.0
CB E:ASN200 4.8 22.4 1.0
O E:PHE213 4.8 26.8 1.0

Reference:

F.Duclos, L.M.Abell, D.G.Harden, K.Pike, K.Nowak, G.A.Locke, G.J.Duke, X.Liu, G.Fernando, S.A.Shaw, B.P.Vokits, N.R.Wurtz, A.Viet, M.N.Valente, S.Stachura, P.Sleph, J.A.Khan, J.Gao, A.R.Dongre, L.Zhao, R.R.Wexler, D.A.Gordon, E.K.Kick. Triazolopyrimidines Identified As Reversible Myeloperoxidase Inhibitors. Medchemcomm V. 8 2093 2017.
ISSN: ISSN 2040-2503
PubMed: 30108726
DOI: 10.1039/C7MD00268H
Page generated: Fri Jul 26 19:18:19 2024

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