Chlorine in PDB 7ni1: Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
Enzymatic activity of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
All present enzymatic activity of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9:
1.11.2.2;
Protein crystallography data
The structure of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9, PDB code: 7ni1
was solved by
T.Sjogren,
T.Inghardt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.24 /
2.11
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.22,
63.82,
111.34,
90,
97.24,
90
|
R / Rfree (%)
|
21.7 /
25.6
|
Other elements in 7ni1:
The structure of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
(pdb code 7ni1). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9, PDB code: 7ni1:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 1 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
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 Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl201
b:11.0
occ:0.96
|
N
|
A:TRP32
|
3.0
|
18.5
|
1.0
|
N
|
C:VAL327
|
3.3
|
9.3
|
1.0
|
O
|
A:HOH314
|
3.3
|
15.9
|
1.0
|
CH2
|
C:TRP436
|
3.6
|
13.2
|
1.0
|
CA
|
A:ARG31
|
3.7
|
16.3
|
1.0
|
CB
|
C:ASN326
|
3.8
|
3.0
|
1.0
|
N
|
C:ASN326
|
3.8
|
8.6
|
1.0
|
CB
|
C:VAL327
|
3.8
|
12.2
|
1.0
|
C
|
A:ARG31
|
3.8
|
21.2
|
1.0
|
CG1
|
C:VAL327
|
3.9
|
11.7
|
1.0
|
CZ2
|
C:TRP436
|
4.0
|
13.8
|
1.0
|
O
|
A:VAL30
|
4.0
|
15.4
|
1.0
|
CA
|
A:TRP32
|
4.0
|
17.4
|
1.0
|
CB
|
A:TRP32
|
4.0
|
16.2
|
1.0
|
N
|
A:LEU33
|
4.1
|
12.8
|
1.0
|
CA
|
C:ASN326
|
4.1
|
6.7
|
1.0
|
C
|
C:ASN326
|
4.1
|
11.8
|
1.0
|
CA
|
C:VAL327
|
4.1
|
9.5
|
1.0
|
CB
|
C:ALA325
|
4.3
|
11.1
|
1.0
|
CD2
|
C:LEU430
|
4.3
|
14.5
|
1.0
|
C
|
C:ALA325
|
4.5
|
12.3
|
1.0
|
O
|
A:LEU33
|
4.5
|
17.1
|
1.0
|
CB
|
A:ARG31
|
4.5
|
15.0
|
1.0
|
C
|
A:TRP32
|
4.5
|
18.2
|
1.0
|
CD
|
A:ARG31
|
4.6
|
17.5
|
1.0
|
CG
|
A:TRP32
|
4.7
|
17.8
|
1.0
|
N
|
A:ARG31
|
4.7
|
16.4
|
1.0
|
CZ3
|
C:TRP436
|
4.8
|
13.2
|
1.0
|
CA
|
C:ALA325
|
4.8
|
10.2
|
1.0
|
C
|
A:VAL30
|
4.8
|
17.1
|
1.0
|
CG
|
A:ARG31
|
4.9
|
18.1
|
1.0
|
NH1
|
A:ARG31
|
5.0
|
5.8
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 2 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
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 Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:21.7
occ:1.00
|
N20
|
C:UEB606
|
3.0
|
24.5
|
1.0
|
O
|
A:HOH308
|
3.3
|
10.4
|
1.0
|
CE1
|
A:HIS95
|
3.4
|
13.6
|
1.0
|
NE2
|
A:GLN91
|
3.4
|
13.2
|
1.0
|
CG
|
C:GLU242
|
3.4
|
19.5
|
1.0
|
NE2
|
A:HIS95
|
3.6
|
13.8
|
1.0
|
CD
|
C:GLU242
|
3.6
|
21.6
|
1.0
|
CB
|
C:GLU242
|
3.7
|
17.4
|
1.0
|
O22
|
C:UEB606
|
3.7
|
18.2
|
1.0
|
CD
|
C:ARG239
|
3.8
|
19.3
|
1.0
|
C21
|
C:UEB606
|
3.8
|
20.6
|
1.0
|
S19
|
C:UEB606
|
3.8
|
27.5
|
1.0
|
C18
|
C:UEB606
|
3.8
|
27.5
|
1.0
|
CB
|
C:ARG239
|
3.9
|
4.6
|
1.0
|
OE1
|
C:GLU242
|
3.9
|
7.2
|
1.0
|
CG
|
C:ARG239
|
4.0
|
21.8
|
1.0
|
CHB
|
A:HEM203
|
4.1
|
20.8
|
1.0
|
OE2
|
C:GLU242
|
4.1
|
15.6
|
1.0
|
C1B
|
A:HEM203
|
4.1
|
20.4
|
1.0
|
C4A
|
A:HEM203
|
4.3
|
20.5
|
1.0
|
NB
|
A:HEM203
|
4.5
|
19.9
|
1.0
|
NA
|
A:HEM203
|
4.5
|
20.5
|
1.0
|
C2B
|
A:HEM203
|
4.5
|
20.5
|
1.0
|
CD
|
A:GLN91
|
4.5
|
17.3
|
1.0
|
ND1
|
A:HIS95
|
4.6
|
14.4
|
1.0
|
CD2
|
C:LEU246
|
4.8
|
10.2
|
1.0
|
O
|
C:ARG239
|
4.8
|
12.3
|
1.0
|
CG
|
A:GLN91
|
4.8
|
8.1
|
1.0
|
C3A
|
A:HEM203
|
4.9
|
21.0
|
1.0
|
NE
|
C:ARG239
|
4.9
|
21.1
|
1.0
|
CD2
|
A:HIS95
|
4.9
|
14.3
|
1.0
|
CMB
|
A:HEM203
|
5.0
|
22.1
|
1.0
|
C1A
|
A:HEM203
|
5.0
|
20.6
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 3 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
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 Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl201
b:12.9
occ:1.00
|
N
|
B:TRP32
|
3.2
|
17.6
|
1.0
|
N
|
D:VAL327
|
3.2
|
10.6
|
1.0
|
O
|
B:HOH327
|
3.3
|
20.7
|
1.0
|
CH2
|
D:TRP436
|
3.6
|
15.3
|
1.0
|
CA
|
B:ARG31
|
3.7
|
15.0
|
1.0
|
N
|
D:ASN326
|
3.7
|
12.6
|
1.0
|
CB
|
D:ASN326
|
3.7
|
16.1
|
1.0
|
CB
|
D:VAL327
|
3.8
|
11.8
|
1.0
|
C
|
B:ARG31
|
3.9
|
18.9
|
1.0
|
CZ2
|
D:TRP436
|
3.9
|
15.6
|
1.0
|
CG1
|
D:VAL327
|
3.9
|
11.1
|
1.0
|
O
|
B:VAL30
|
4.0
|
15.1
|
1.0
|
CA
|
D:ASN326
|
4.0
|
12.8
|
1.0
|
C
|
D:ASN326
|
4.1
|
15.6
|
1.0
|
CA
|
D:VAL327
|
4.1
|
8.2
|
1.0
|
N
|
B:LEU33
|
4.1
|
13.2
|
1.0
|
CA
|
B:TRP32
|
4.2
|
18.7
|
1.0
|
CB
|
B:TRP32
|
4.2
|
19.4
|
1.0
|
CD2
|
D:LEU430
|
4.3
|
15.4
|
1.0
|
CB
|
D:ALA325
|
4.4
|
9.7
|
1.0
|
O
|
B:LEU33
|
4.4
|
17.4
|
1.0
|
CB
|
B:ARG31
|
4.4
|
16.0
|
1.0
|
C
|
D:ALA325
|
4.4
|
14.5
|
1.0
|
CD
|
B:ARG31
|
4.5
|
20.4
|
1.0
|
C
|
B:TRP32
|
4.7
|
18.6
|
1.0
|
N
|
B:ARG31
|
4.7
|
14.8
|
1.0
|
CZ3
|
D:TRP436
|
4.7
|
14.8
|
1.0
|
CA
|
D:ALA325
|
4.8
|
8.7
|
1.0
|
CG
|
B:ARG31
|
4.8
|
24.1
|
1.0
|
C
|
B:VAL30
|
4.8
|
17.0
|
1.0
|
CG
|
B:TRP32
|
4.9
|
22.0
|
1.0
|
NH1
|
B:ARG31
|
4.9
|
11.6
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 4 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
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 Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl202
b:21.7
occ:1.00
|
O
|
B:HOH337
|
2.8
|
18.7
|
1.0
|
NE2
|
B:GLN91
|
3.2
|
15.9
|
1.0
|
N20
|
D:UEB606
|
3.3
|
19.2
|
1.0
|
CE1
|
B:HIS95
|
3.3
|
18.8
|
1.0
|
CG
|
D:GLU242
|
3.4
|
21.3
|
1.0
|
NE2
|
B:HIS95
|
3.5
|
18.8
|
1.0
|
CD
|
D:GLU242
|
3.6
|
29.7
|
1.0
|
CB
|
D:GLU242
|
3.7
|
20.6
|
1.0
|
CD
|
D:ARG239
|
3.8
|
8.5
|
1.0
|
S19
|
D:UEB606
|
3.9
|
19.9
|
1.0
|
CHB
|
B:HEM203
|
3.9
|
23.3
|
1.0
|
C1B
|
B:HEM203
|
3.9
|
22.9
|
1.0
|
OE2
|
D:GLU242
|
3.9
|
24.5
|
1.0
|
CB
|
D:ARG239
|
4.0
|
17.2
|
1.0
|
O22
|
D:UEB606
|
4.0
|
22.4
|
1.0
|
OE1
|
D:GLU242
|
4.1
|
22.5
|
1.0
|
C18
|
D:UEB606
|
4.1
|
18.4
|
1.0
|
C21
|
D:UEB606
|
4.1
|
20.6
|
1.0
|
C4A
|
B:HEM203
|
4.1
|
22.9
|
1.0
|
CG
|
D:ARG239
|
4.2
|
17.1
|
1.0
|
NB
|
B:HEM203
|
4.2
|
22.6
|
1.0
|
CD
|
B:GLN91
|
4.3
|
23.6
|
1.0
|
C2B
|
B:HEM203
|
4.3
|
23.1
|
1.0
|
NA
|
B:HEM203
|
4.3
|
22.9
|
1.0
|
ND1
|
B:HIS95
|
4.6
|
19.4
|
1.0
|
CG
|
B:GLN91
|
4.6
|
11.3
|
1.0
|
C4B
|
B:HEM203
|
4.7
|
23.0
|
1.0
|
CD2
|
D:LEU246
|
4.7
|
20.3
|
1.0
|
C3A
|
B:HEM203
|
4.8
|
23.4
|
1.0
|
CMB
|
B:HEM203
|
4.8
|
24.7
|
1.0
|
CD2
|
B:HIS95
|
4.8
|
19.4
|
1.0
|
C3B
|
B:HEM203
|
4.9
|
23.3
|
1.0
|
FE
|
B:HEM203
|
4.9
|
22.8
|
1.0
|
NE
|
D:ARG239
|
4.9
|
9.3
|
1.0
|
O
|
D:ARG239
|
4.9
|
21.7
|
1.0
|
C1A
|
B:HEM203
|
4.9
|
23.1
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 5 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl602
b:23.8
occ:0.96
|
NE
|
C:ARG382
|
3.2
|
28.0
|
1.0
|
N
|
C:THR544
|
3.3
|
16.6
|
1.0
|
NH2
|
C:ARG382
|
3.4
|
22.3
|
1.0
|
CA
|
C:ILE543
|
3.6
|
16.9
|
1.0
|
O
|
C:HOH932
|
3.7
|
28.2
|
1.0
|
CZ
|
C:ARG382
|
3.7
|
39.9
|
1.0
|
CG2
|
C:ILE543
|
3.8
|
16.9
|
1.0
|
OG1
|
C:THR544
|
3.9
|
20.2
|
1.0
|
N
|
C:THR545
|
3.9
|
18.0
|
1.0
|
C
|
C:ILE543
|
4.0
|
19.8
|
1.0
|
CB
|
C:ILE543
|
4.1
|
18.9
|
1.0
|
O
|
C:ASN348
|
4.1
|
31.7
|
1.0
|
CA
|
C:ASN348
|
4.2
|
25.4
|
1.0
|
CD
|
C:ARG382
|
4.2
|
22.0
|
1.0
|
CA
|
C:THR544
|
4.4
|
15.5
|
1.0
|
CB
|
C:ASN348
|
4.4
|
23.8
|
1.0
|
O
|
C:GLY542
|
4.4
|
23.5
|
1.0
|
CE1
|
C:TYR350
|
4.4
|
33.3
|
1.0
|
CG1
|
C:ILE543
|
4.4
|
18.7
|
1.0
|
O
|
C:THR545
|
4.5
|
24.5
|
1.0
|
C
|
C:ASN348
|
4.6
|
30.9
|
1.0
|
C
|
C:THR544
|
4.6
|
19.3
|
1.0
|
CB
|
C:THR545
|
4.7
|
28.2
|
1.0
|
N
|
C:ILE543
|
4.7
|
18.2
|
1.0
|
CB
|
C:THR544
|
4.7
|
23.5
|
1.0
|
CA
|
C:THR545
|
4.8
|
18.9
|
1.0
|
C
|
C:GLY542
|
5.0
|
23.4
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 6 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl603
b:33.9
occ:0.99
|
N
|
C:GLN201
|
3.4
|
28.0
|
1.0
|
N
|
C:PHE213
|
3.4
|
16.7
|
1.0
|
CA
|
C:PRO212
|
3.7
|
18.0
|
1.0
|
CA
|
C:ASN200
|
3.8
|
23.2
|
1.0
|
CB
|
C:PRO212
|
3.9
|
19.9
|
1.0
|
CG
|
C:ASN200
|
3.9
|
34.2
|
1.0
|
OD1
|
C:ASN200
|
4.0
|
16.1
|
1.0
|
ND2
|
C:ASN200
|
4.1
|
24.5
|
1.0
|
C
|
C:PRO212
|
4.1
|
20.5
|
1.0
|
C
|
C:ASN200
|
4.1
|
28.7
|
1.0
|
CD2
|
C:PHE213
|
4.1
|
16.5
|
1.0
|
CB
|
C:GLN201
|
4.2
|
29.7
|
1.0
|
CA
|
C:GLN201
|
4.3
|
28.4
|
1.0
|
CB
|
C:PHE213
|
4.4
|
15.7
|
1.0
|
CG
|
C:GLN201
|
4.4
|
36.6
|
1.0
|
CB
|
C:ASN200
|
4.4
|
20.5
|
1.0
|
CA
|
C:PHE213
|
4.5
|
15.4
|
1.0
|
CG
|
C:PHE213
|
4.5
|
15.7
|
1.0
|
O
|
C:VAL199
|
4.6
|
25.3
|
1.0
|
N
|
C:ARG202
|
4.7
|
26.1
|
1.0
|
O
|
C:PHE213
|
4.7
|
23.7
|
1.0
|
N
|
C:ASN200
|
4.9
|
22.9
|
1.0
|
CE2
|
C:PHE213
|
5.0
|
19.1
|
1.0
|
C
|
C:GLN201
|
5.0
|
31.7
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 7ni1
Go back to
Chlorine Binding Sites List in 7ni1
Chlorine binding site 7 out
of 7 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 9 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl602
b:81.3
occ:0.96
|
O
|
D:HOH868
|
3.1
|
9.4
|
1.0
|
O
|
D:HOH830
|
3.4
|
26.3
|
1.0
|
CG
|
D:GLN201
|
3.7
|
39.1
|
1.0
|
CB
|
D:GLN201
|
4.1
|
29.8
|
1.0
|
CB
|
D:PRO212
|
4.7
|
23.6
|
1.0
|
N
|
D:GLN201
|
4.8
|
28.2
|
1.0
|
|
Reference:
T.Inghardt,
T.Antonsson,
C.Ericsson,
D.Hovdal,
P.Johannesson,
C.Johansson,
U.Jurva,
J.Kajanus,
B.Kull,
E.Michaelsson,
A.Pettersen,
T.Sjogren,
H.Sorensen,
K.Westerlund,
E.L.Lindstedt.
Discovery of AZD4831, A Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As A Potential Treatment For Heart Failure with Preserved Ejection Fraction. J.Med.Chem. V. 65 11485 2022.
ISSN: ISSN 0022-2623
PubMed: 36005476
DOI: 10.1021/ACS.JMEDCHEM.1C02141
Page generated: Tue Jul 30 00:55:25 2024
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