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Chlorine in PDB 5r95: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha, PDB code: 5r95 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) 50.98 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.930, 86.100, 126.520, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 20.4

Other elements in 5r95:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha (pdb code 5r95). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 in Complex with Map Kinase P38-Alpha, PDB code: 5r95:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5r95

Go back to Chlorine Binding Sites List in 5r95
Chlorine binding site 1 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:44.3
occ:1.00
 O A:HOH835 2.7 34.4 1.0
O A:HOH673 2.9 33.9 1.0
O A:HOH772 3.0 35.0 1.0
N A:ARG23 3.1 22.8 1.0
N A:GLU22 3.5 22.3 1.0
CB A:ARG23 3.6 28.1 1.0
CB A:PRO6 3.7 37.0 1.0
CB A:PRO21 3.7 23.9 1.0
CA A:ARG23 3.9 23.6 1.0
C A:GLU22 4.0 24.8 1.0
CG A:ARG23 4.0 26.1 1.0
CA A:GLU22 4.0 24.8 1.0
CB A:GLU22 4.0 24.4 1.0
C A:PRO21 4.0 23.9 1.0
CA A:PRO21 4.3 21.5 1.0
CD A:ARG23 4.3 26.5 1.0
O A:THR7 4.4 30.4 1.0
O A:HOH705 4.6 32.6 1.0
CA A:PRO6 4.8 35.9 1.0
CG A:PRO6 4.8 38.4 1.0
O A:PRO21 4.8 22.8 1.0
N A:THR7 4.9 28.9 1.0
CG A:GLU22 4.9 26.7 1.0

Chlorine binding site 2 out of 7 in 5r95

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Chlorine binding site 2 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:40.2
occ:1.00
 N A:ASN100 3.2 32.0 1.0
N A:ASP101 3.2 32.2 1.0
OG1 A:THR91 3.4 27.3 1.0
CB A:ALA93 3.6 27.9 1.0
O A:GLU98 3.6 38.8 1.0
N A:ALA93 3.8 29.7 1.0
CA A:ASN100 3.9 33.2 1.0
CB A:ASP101 4.0 31.2 1.0
CG A:PRO92 4.0 32.7 1.0
C A:ASN100 4.0 36.4 1.0
CD A:PRO92 4.0 26.3 1.0
CA A:ASP101 4.1 31.4 1.0
CA A:ALA93 4.1 32.2 1.0
CB A:ASN100 4.1 39.1 1.0
C A:PHE99 4.1 36.8 1.0
O A:ASP101 4.2 27.9 1.0
CA A:PHE99 4.2 29.6 1.0
CG A:ASP101 4.5 41.7 1.0
OD2 A:ASP101 4.5 40.4 1.0
N A:PRO92 4.6 26.5 1.0
C A:GLU98 4.6 39.2 1.0
C A:ASP101 4.6 24.0 1.0
C A:PRO92 4.6 32.6 1.0
ND2 A:ASN100 4.7 47.5 1.0
CD1 A:PHE99 4.7 29.1 1.0
CB A:THR91 4.8 26.2 1.0
N A:PHE99 4.9 36.0 1.0
CG A:ASN100 4.9 49.9 1.0
CB A:PRO92 5.0 31.2 1.0
CA A:PRO92 5.0 28.4 1.0

Chlorine binding site 3 out of 7 in 5r95

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Chlorine binding site 3 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:49.1
occ:1.00
 O A:HOH622 2.9 37.0 1.0
O A:HOH507 3.0 35.4 1.0
N A:GLY85 3.2 26.1 1.0
CD2 A:HIS107 3.6 36.9 1.0
CE A:LYS165 3.7 37.6 1.0
CD A:LYS165 3.9 31.5 1.0
O A:VAL83 4.0 22.2 1.0
CA A:ILE84 4.0 25.5 1.0
CA A:GLY85 4.0 29.4 1.0
C A:ILE84 4.1 26.0 1.0
NZ A:LYS165 4.2 39.7 1.0
O A:GLY85 4.2 25.1 1.0
O A:HOH784 4.4 45.5 1.0
CG A:HIS107 4.5 35.4 1.0
C A:GLY85 4.5 25.9 1.0
NE2 A:HIS107 4.6 39.1 1.0
CG1 A:ILE84 4.6 30.0 1.0
CB A:HIS107 4.7 34.6 1.0
O A:HOH605 4.7 23.9 1.0
CE A:MET109 4.8 41.3 1.0
C A:VAL83 4.9 21.4 1.0
N A:ILE84 4.9 21.4 1.0
CB A:ILE84 5.0 27.1 1.0

Chlorine binding site 4 out of 7 in 5r95

Go back to Chlorine Binding Sites List in 5r95
Chlorine binding site 4 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:30.6
occ:0.59
 N A:ASP324 3.0 22.8 1.0
O A:HOH607 3.2 37.4 1.0
CB A:ASP324 3.6 24.9 1.0
NH2 A:ARG73 3.6 25.2 1.0
O A:PRO322 3.7 23.8 1.0
CA A:TYR323 3.7 22.0 1.0
C A:TYR323 3.9 24.3 1.0
CA A:ASP324 3.9 25.8 1.0
CD1 A:TYR323 4.2 23.4 1.0
C A:PRO322 4.5 23.8 1.0
N A:TYR323 4.5 21.3 1.0
O A:HOH570 4.5 34.0 1.0
O A:ASP324 4.5 24.8 1.0
C A:ASP324 4.7 23.4 1.0
CE1 A:HIS77 4.7 26.6 1.0
ND1 A:HIS77 4.8 26.0 1.0
CZ A:ARG73 4.8 23.5 1.0
CB A:TYR323 4.8 23.2 1.0
CG A:TYR323 4.9 22.6 1.0
CE1 A:TYR323 4.9 24.4 1.0

Chlorine binding site 5 out of 7 in 5r95

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Chlorine binding site 5 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.6
occ:0.79
 O A:HOH684 2.9 36.0 1.0
OG A:SER154 3.3 23.2 1.0
N A:SER154 3.3 21.6 1.0
ND2 A:ASN114 3.5 44.5 1.0
CB A:SER154 3.6 23.5 1.0
CD A:PRO153 3.6 20.8 1.0
N A:PRO153 3.8 19.3 1.0
CG A:LYS152 3.8 21.6 1.0
CB A:LYS152 3.9 22.5 1.0
CD A:LYS152 4.0 23.8 1.0
CA A:SER154 4.1 25.3 1.0
CB A:PRO153 4.1 25.5 1.0
O A:HOH794 4.2 47.1 1.0
C A:PRO153 4.2 21.5 1.0
CA A:PRO153 4.3 21.7 1.0
OD1 A:ASN114 4.3 53.3 1.0
C A:LYS152 4.3 20.7 1.0
CG A:ASN114 4.3 43.0 1.0
CG A:PRO153 4.4 22.9 1.0
CB A:ALA184 4.4 25.2 1.0
CE1 A:TYR188 4.4 16.9 1.0
CA A:LYS152 4.7 23.9 1.0
CE A:LYS152 4.7 30.0 1.0
OH A:TYR188 4.8 23.7 1.0
CZ A:TYR188 4.9 21.6 1.0

Chlorine binding site 6 out of 7 in 5r95

Go back to Chlorine Binding Sites List in 5r95
Chlorine binding site 6 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:42.2
occ:0.67
 N A:GLN264 3.0 30.4 1.0
CA A:ALA263 3.5 33.0 1.0
CB A:ALA263 3.7 34.2 1.0
C A:ALA263 3.8 31.6 1.0
CB A:GLN264 4.1 32.1 1.0
CG A:GLN264 4.1 37.9 1.0
CA A:GLN264 4.1 28.9 1.0
O A:HOH790 4.4 54.8 1.0
O A:GLN264 4.6 28.6 1.0
N A:ALA263 4.8 28.1 1.0
NE2 A:GLN264 4.8 36.4 1.0
C A:GLN264 4.9 26.9 1.0
O A:LEU262 4.9 32.2 1.0
CD A:GLN264 4.9 43.1 1.0
O A:ALA263 5.0 28.1 1.0

Chlorine binding site 7 out of 7 in 5r95

Go back to Chlorine Binding Sites List in 5r95
Chlorine binding site 7 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 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 7 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL093 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:73.4
occ:0.98
 N A:ILE334 3.0 33.3 1.0
CG1 A:ILE334 3.6 37.6 1.0
CB A:ILE334 3.7 38.3 1.0
CB A:LEU333 3.7 33.3 1.0
CA A:LEU333 3.7 36.2 1.0
O A:HOH723 3.7 42.6 1.0
CD1 A:ILE62 3.8 46.7 1.0
CG1 A:ILE62 3.8 36.9 1.0
C A:LEU333 3.8 32.0 1.0
CA A:ILE334 3.9 30.5 1.0
CD2 A:LEU333 4.2 43.7 1.0
CD1 A:ILE334 4.3 43.3 1.0
CG A:LEU333 4.5 37.8 1.0
N A:ASP335 5.0 29.4 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 15:59:28 2024

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