Chlorine in PDB 5r9d: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha:
2.7.11.24;
Protein crystallography data
The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha, PDB code: 5r9d
was solved by
G.F.De Nicola,
C.E.Nichols,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
71.34 /
1.69
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.620,
86.040,
127.640,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
21.3
|
Other elements in 5r9d:
The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
(pdb code 5r9d). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha, PDB code: 5r9d:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 5r9d
Go back to
Chlorine Binding Sites List in 5r9d
Chlorine binding site 1 out
of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:44.7
occ:1.00
|
O
|
A:HOH756
|
2.7
|
31.5
|
1.0
|
O
|
A:HOH718
|
3.0
|
34.5
|
1.0
|
O
|
A:HOH614
|
3.0
|
31.7
|
1.0
|
N
|
A:ARG23
|
3.0
|
22.1
|
1.0
|
N
|
A:GLU22
|
3.5
|
24.5
|
1.0
|
CB
|
A:ARG23
|
3.6
|
27.3
|
1.0
|
CB
|
A:PRO6
|
3.8
|
34.8
|
1.0
|
CB
|
A:PRO21
|
3.8
|
22.8
|
1.0
|
CA
|
A:ARG23
|
3.8
|
23.2
|
1.0
|
C
|
A:GLU22
|
3.9
|
24.4
|
1.0
|
CB
|
A:GLU22
|
3.9
|
19.0
|
1.0
|
CA
|
A:GLU22
|
3.9
|
23.2
|
1.0
|
C
|
A:PRO21
|
4.1
|
23.9
|
1.0
|
CG
|
A:ARG23
|
4.2
|
27.9
|
1.0
|
CA
|
A:PRO21
|
4.4
|
21.9
|
1.0
|
O
|
A:THR7
|
4.5
|
28.4
|
1.0
|
CD
|
A:ARG23
|
4.6
|
25.9
|
1.0
|
O
|
A:PRO21
|
4.8
|
20.9
|
1.0
|
CA
|
A:PRO6
|
4.9
|
30.8
|
1.0
|
CG
|
A:PRO6
|
4.9
|
32.0
|
1.0
|
CG
|
A:GLU22
|
4.9
|
28.1
|
1.0
|
O
|
A:HOH655
|
4.9
|
34.8
|
1.0
|
OE1
|
A:GLU22
|
4.9
|
26.6
|
1.0
|
N
|
A:THR7
|
5.0
|
26.1
|
1.0
|
O
|
A:GLU22
|
5.0
|
22.6
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 5r9d
Go back to
Chlorine Binding Sites List in 5r9d
Chlorine binding site 2 out
of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:43.2
occ:1.00
|
N
|
A:ASN100
|
3.2
|
33.2
|
0.5
|
N
|
A:ASN100
|
3.2
|
33.2
|
0.5
|
N
|
A:ASP101
|
3.2
|
30.6
|
1.0
|
OG1
|
A:THR91
|
3.5
|
28.3
|
1.0
|
O
|
A:GLU98
|
3.6
|
37.3
|
1.0
|
CB
|
A:ALA93
|
3.7
|
31.6
|
1.0
|
CB
|
A:ASP101
|
3.9
|
33.2
|
1.0
|
N
|
A:ALA93
|
3.9
|
31.4
|
1.0
|
CA
|
A:ASN100
|
3.9
|
33.3
|
0.5
|
CA
|
A:ASN100
|
3.9
|
33.4
|
0.5
|
CG
|
A:PRO92
|
3.9
|
35.1
|
1.0
|
C
|
A:ASN100
|
3.9
|
34.0
|
0.5
|
C
|
A:ASN100
|
4.0
|
34.0
|
0.5
|
CA
|
A:ASP101
|
4.1
|
30.7
|
1.0
|
C
|
A:PHE99
|
4.1
|
31.6
|
1.0
|
CB
|
A:ASN100
|
4.2
|
37.9
|
0.5
|
CD
|
A:PRO92
|
4.2
|
28.1
|
1.0
|
CA
|
A:PHE99
|
4.2
|
34.7
|
1.0
|
O
|
A:ASP101
|
4.2
|
25.4
|
1.0
|
CA
|
A:ALA93
|
4.2
|
33.0
|
1.0
|
CB
|
A:ASN100
|
4.2
|
37.9
|
0.5
|
OD2
|
A:ASP101
|
4.3
|
42.5
|
1.0
|
CG
|
A:ASP101
|
4.4
|
45.4
|
1.0
|
C
|
A:GLU98
|
4.6
|
42.1
|
1.0
|
N
|
A:PRO92
|
4.6
|
25.0
|
1.0
|
C
|
A:ASP101
|
4.6
|
25.5
|
1.0
|
C
|
A:PRO92
|
4.7
|
35.5
|
1.0
|
CD1
|
A:PHE99
|
4.8
|
31.2
|
1.0
|
N
|
A:PHE99
|
4.9
|
34.3
|
1.0
|
CB
|
A:THR91
|
4.9
|
26.8
|
1.0
|
CB
|
A:PRO92
|
4.9
|
31.2
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 5r9d
Go back to
Chlorine Binding Sites List in 5r9d
Chlorine binding site 3 out
of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl404
b:31.0
occ:0.60
|
O
|
A:HOH607
|
2.9
|
35.2
|
1.0
|
N
|
A:ASP324
|
3.0
|
24.8
|
1.0
|
NH2
|
A:ARG73
|
3.5
|
26.3
|
1.0
|
CB
|
A:ASP324
|
3.6
|
22.4
|
1.0
|
CA
|
A:TYR323
|
3.7
|
23.6
|
1.0
|
O
|
A:PRO322
|
3.8
|
24.5
|
1.0
|
C
|
A:TYR323
|
3.8
|
25.2
|
1.0
|
CA
|
A:ASP324
|
3.8
|
24.5
|
1.0
|
CD1
|
A:TYR323
|
4.4
|
23.6
|
1.0
|
O
|
A:ASP324
|
4.5
|
27.8
|
1.0
|
N
|
A:TYR323
|
4.5
|
22.1
|
1.0
|
C
|
A:PRO322
|
4.5
|
23.0
|
1.0
|
O
|
A:HOH746
|
4.5
|
28.4
|
1.0
|
O
|
A:HOH744
|
4.5
|
43.6
|
1.0
|
O
|
A:HOH526
|
4.6
|
31.1
|
1.0
|
CZ
|
A:ARG73
|
4.6
|
25.4
|
1.0
|
C
|
A:ASP324
|
4.7
|
25.0
|
1.0
|
CB
|
A:TYR323
|
4.8
|
22.1
|
1.0
|
ND1
|
A:HIS77
|
4.8
|
30.4
|
1.0
|
CG
|
A:TYR323
|
4.9
|
24.0
|
1.0
|
CE1
|
A:HIS77
|
4.9
|
26.0
|
1.0
|
CG
|
A:ASP324
|
5.0
|
28.0
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 5r9d
Go back to
Chlorine Binding Sites List in 5r9d
Chlorine binding site 4 out
of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl405
b:28.0
occ:0.79
|
O
|
A:HOH619
|
3.1
|
31.4
|
1.0
|
OG
|
A:SER154
|
3.1
|
25.4
|
1.0
|
ND2
|
A:ASN114
|
3.2
|
46.5
|
1.0
|
N
|
A:SER154
|
3.2
|
22.7
|
1.0
|
O
|
A:HOH684
|
3.4
|
40.1
|
1.0
|
CB
|
A:SER154
|
3.5
|
25.3
|
1.0
|
CD
|
A:PRO153
|
3.6
|
19.9
|
1.0
|
N
|
A:PRO153
|
3.8
|
19.1
|
1.0
|
CG
|
A:LYS152
|
3.8
|
21.8
|
1.0
|
CD
|
A:LYS152
|
3.8
|
22.8
|
1.0
|
CB
|
A:LYS152
|
3.9
|
21.5
|
1.0
|
CA
|
A:SER154
|
4.0
|
23.3
|
1.0
|
C
|
A:PRO153
|
4.2
|
23.5
|
1.0
|
CB
|
A:PRO153
|
4.2
|
22.6
|
1.0
|
CG
|
A:ASN114
|
4.2
|
47.5
|
1.0
|
CA
|
A:PRO153
|
4.3
|
20.0
|
1.0
|
C
|
A:LYS152
|
4.3
|
20.9
|
1.0
|
CB
|
A:ALA184
|
4.4
|
26.8
|
1.0
|
CG
|
A:PRO153
|
4.4
|
24.3
|
1.0
|
CE1
|
A:TYR188
|
4.4
|
20.3
|
1.0
|
OD1
|
A:ASN114
|
4.5
|
54.7
|
1.0
|
CE
|
A:LYS152
|
4.7
|
26.2
|
1.0
|
CA
|
A:LYS152
|
4.7
|
18.8
|
1.0
|
O
|
A:LYS152
|
4.9
|
22.4
|
1.0
|
OH
|
A:TYR188
|
5.0
|
23.2
|
1.0
|
CZ
|
A:TYR188
|
5.0
|
23.1
|
1.0
|
O
|
A:ALA184
|
5.0
|
24.4
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 5r9d
Go back to
Chlorine Binding Sites List in 5r9d
Chlorine binding site 5 out
of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment S00888C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl406
b:45.5
occ:0.63
|
O
|
A:HOH711
|
2.9
|
44.8
|
1.0
|
N
|
A:GLN264
|
3.1
|
28.4
|
1.0
|
CA
|
A:ALA263
|
3.8
|
29.8
|
1.0
|
CB
|
A:GLN264
|
3.9
|
32.8
|
1.0
|
C
|
A:ALA263
|
3.9
|
27.9
|
1.0
|
CG
|
A:GLN264
|
4.0
|
40.1
|
1.0
|
CA
|
A:GLN264
|
4.1
|
25.1
|
1.0
|
CB
|
A:ALA263
|
4.1
|
30.5
|
1.0
|
NE2
|
A:GLN264
|
4.6
|
36.5
|
1.0
|
O
|
A:GLN264
|
4.7
|
28.4
|
1.0
|
CD
|
A:GLN264
|
4.8
|
39.9
|
1.0
|
C
|
A:GLN264
|
4.9
|
25.3
|
1.0
|
O
|
A:LEU262
|
4.9
|
29.2
|
1.0
|
|
Reference:
C.Nichols,
J.Ng,
A.Keshu,
G.Kelly,
M.R.Conte,
M.S.Marber,
F.Fraternali,
G.F.De Nicola.
Mining the Pdb For Tractable Cases Where X-Ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated By IL1 Beta-IL1R and P38 Alpha-TAB1 Complexes. J.Med.Chem. V. 63 7559 2020.
ISSN: ISSN 0022-2623
PubMed: 32543856
DOI: 10.1021/ACS.JMEDCHEM.0C00403
Page generated: Fri Jul 26 16:03:07 2024
|