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Chlorine in PDB 5r96: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 KCL095 in Complex with Map Kinase P38-Alpha, PDB code: 5r96 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) 29.34 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.021, 86.170, 127.337, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.8

Other elements in 5r96:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 in Complex with Map Kinase P38-Alpha (pdb code 5r96). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 in Complex with Map Kinase P38-Alpha, PDB code: 5r96:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r96

Go back to Chlorine Binding Sites List in 5r96
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 KCL095 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:38.2
occ:0.87
 CL A:SQ7401 0.0 38.2 0.9
C A:SQ7401 1.7 25.3 0.9
C1 A:SQ7401 2.7 20.5 0.9
C8 A:SQ7401 2.7 26.3 0.9
C1 A:DMS410 3.3 37.6 1.0
O A:HOH621 3.8 37.3 1.0
C2 A:SQ7401 4.0 21.8 0.9
C7 A:SQ7401 4.0 24.0 0.9
C3 A:SQ7401 4.5 23.3 0.9
S A:DMS410 4.6 58.2 1.0
C2 A:DMS410 4.6 46.5 1.0

Chlorine binding site 2 out of 6 in 5r96

Go back to Chlorine Binding Sites List in 5r96
Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 KCL095 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:48.1
occ:1.00
 O A:HOH777 2.7 36.6 1.0
O A:HOH618 3.1 34.1 1.0
N A:ARG23 3.1 26.4 1.0
O A:HOH739 3.3 41.6 1.0
N A:GLU22 3.5 25.1 1.0
CB A:ARG23 3.6 30.8 1.0
CB A:PRO6 3.8 36.1 1.0
CB A:PRO21 3.8 26.0 1.0
CA A:ARG23 3.9 23.8 1.0
CG A:ARG23 4.0 29.0 1.0
C A:GLU22 4.0 24.1 1.0
CA A:GLU22 4.0 25.1 1.0
C A:PRO21 4.0 26.4 1.0
CB A:GLU22 4.0 26.1 1.0
CD A:ARG23 4.3 30.0 1.0
CA A:PRO21 4.3 22.2 1.0
O A:THR7 4.5 29.9 1.0
O A:HOH664 4.7 38.2 1.0
O A:PRO21 4.8 22.6 1.0
CA A:PRO6 4.8 35.6 1.0
CG A:PRO6 4.9 34.9 1.0
N A:THR7 4.9 31.4 1.0
CG A:GLU22 5.0 30.1 1.0

Chlorine binding site 3 out of 6 in 5r96

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Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 KCL095 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:41.7
occ:1.00
 N A:ASN100 3.2 33.9 1.0
N A:ASP101 3.2 32.1 1.0
OG1 A:THR91 3.5 27.3 1.0
O A:GLU98 3.7 38.0 1.0
CB A:ALA93 3.7 32.9 1.0
CA A:ASN100 3.8 35.9 1.0
CB A:ASP101 3.9 33.0 1.0
N A:ALA93 3.9 31.4 1.0
C A:ASN100 4.0 35.2 1.0
CB A:ASN100 4.0 40.1 1.0
CG A:PRO92 4.0 32.9 1.0
CA A:ASP101 4.0 32.5 1.0
CD A:PRO92 4.1 26.4 1.0
C A:PHE99 4.2 35.9 1.0
CA A:ALA93 4.2 34.4 1.0
O A:ASP101 4.3 29.3 1.0
CA A:PHE99 4.3 31.8 1.0
OD2 A:ASP101 4.3 42.9 1.0
CG A:ASP101 4.4 40.6 1.0
N A:PRO92 4.6 25.5 1.0
C A:ASP101 4.7 25.8 1.0
C A:GLU98 4.7 40.1 1.0
C A:PRO92 4.7 35.5 1.0
CD1 A:PHE99 4.8 29.9 1.0
CB A:THR91 4.9 29.6 1.0
CB A:PRO92 4.9 31.9 1.0
ND2 A:ASN100 4.9 45.0 1.0
N A:PHE99 5.0 35.1 1.0

Chlorine binding site 4 out of 6 in 5r96

Go back to Chlorine Binding Sites List in 5r96
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 KCL095 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:48.3
occ:1.00
 O A:HOH590 2.8 38.2 1.0
O A:HOH573 3.0 37.9 1.0
N A:GLY85 3.1 26.0 1.0
ND1 A:HIS107 3.8 40.1 1.0
CE A:LYS165 3.8 38.0 1.0
CA A:GLY85 3.8 28.2 1.0
CD A:LYS165 4.0 32.9 1.0
O A:VAL83 4.0 23.2 1.0
CD1 A:ILE84 4.0 39.2 1.0
C A:ILE84 4.0 27.5 1.0
CA A:ILE84 4.1 24.4 1.0
NZ A:LYS165 4.2 39.5 1.0
O A:GLY85 4.3 28.2 1.0
O A:HOH754 4.3 40.5 1.0
C A:GLY85 4.4 26.6 1.0
CE1 A:HIS107 4.6 40.5 1.0
O A:HOH595 4.7 23.6 1.0
CG A:HIS107 4.7 38.0 1.0
CB A:HIS107 4.8 36.2 1.0
C A:VAL83 4.8 20.3 1.0
CG1 A:ILE84 4.9 33.4 1.0
CE A:MET109 4.9 45.2 1.0
N A:ILE84 4.9 21.8 1.0

Chlorine binding site 5 out of 6 in 5r96

Go back to Chlorine Binding Sites List in 5r96
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 KCL095 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:40.5
occ:1.00
 O A:HOH624 2.7 33.3 1.0
N A:ASP324 3.0 23.3 1.0
NH2 A:ARG73 3.6 25.4 1.0
CB A:ASP324 3.7 25.0 1.0
O A:PRO322 3.7 21.5 1.0
CA A:TYR323 3.7 22.0 1.0
C A:TYR323 3.9 23.6 1.0
CA A:ASP324 4.0 25.0 1.0
CD1 A:TYR323 4.1 25.2 1.0
CE1 A:HIS77 4.4 27.3 1.0
O A:HOH534 4.4 29.0 1.0
C A:PRO322 4.5 22.9 1.0
ND1 A:HIS77 4.5 27.1 1.0
N A:TYR323 4.5 22.0 1.0
O A:ASP324 4.6 28.7 1.0
CB A:TYR323 4.8 21.9 1.0
CG A:TYR323 4.8 22.4 1.0
C A:ASP324 4.8 24.7 1.0
CZ A:ARG73 4.8 26.1 1.0
CE1 A:TYR323 4.8 29.0 1.0

Chlorine binding site 6 out of 6 in 5r96

Go back to Chlorine Binding Sites List in 5r96
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 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 6 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL095 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:28.8
occ:0.71
 O A:HOH613 3.0 31.9 1.0
OG A:SER154 3.2 23.9 1.0
N A:SER154 3.2 22.4 1.0
O A:HOH719 3.3 41.0 1.0
CB A:SER154 3.5 26.5 1.0
ND2 A:ASN114 3.5 41.0 1.0
CD A:PRO153 3.6 23.2 1.0
N A:PRO153 3.7 20.6 1.0
CG A:LYS152 3.8 24.0 1.0
CD A:LYS152 3.9 25.6 1.0
CB A:LYS152 3.9 23.2 1.0
CA A:SER154 4.0 24.0 1.0
C A:PRO153 4.1 24.0 1.0
CB A:PRO153 4.1 26.2 1.0
CA A:PRO153 4.2 20.7 1.0
C A:LYS152 4.3 22.2 1.0
CG A:PRO153 4.3 25.1 1.0
CE1 A:TYR188 4.4 21.6 1.0
CB A:ALA184 4.4 24.7 1.0
OD1 A:ASN114 4.4 53.0 1.0
CG A:ASN114 4.4 45.0 1.0
CE A:LYS152 4.6 29.0 1.0
CA A:LYS152 4.7 22.1 1.0
OH A:TYR188 4.8 23.6 1.0
CZ A:TYR188 4.9 22.5 1.0
O A:LYS152 5.0 22.8 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 15:59:38 2024

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