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Chlorine in PDB 5r9l: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha, PDB code: 5r9l 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) 29.64 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.870, 86.536, 126.182, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20

Other elements in 5r9l:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha (pdb code 5r9l). 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 N14274A in Complex with Map Kinase P38-Alpha, PDB code: 5r9l:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r9l

Go back to Chlorine Binding Sites List in 5r9l
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:31.2
occ:0.60
 O A:HOH792 2.7 32.9 1.0
O A:HOH621 3.0 29.5 1.0
N A:ARG23 3.1 19.9 1.0
O A:HOH748 3.1 32.7 1.0
N A:GLU22 3.5 20.8 1.0
CB A:ARG23 3.7 24.7 1.0
CB A:PRO6 3.8 31.0 1.0
CB A:PRO21 3.8 19.9 1.0
CB A:GLU22 3.9 22.6 1.0
CA A:ARG23 3.9 20.4 1.0
C A:GLU22 3.9 21.0 1.0
CA A:GLU22 4.0 22.0 1.0
CG A:ARG23 4.0 23.9 1.0
C A:PRO21 4.1 21.4 1.0
CA A:PRO21 4.4 20.5 1.0
CD A:ARG23 4.4 23.1 1.0
O A:THR7 4.5 25.0 1.0
O A:HOH696 4.8 30.2 1.0
CA A:PRO6 4.8 30.7 1.0
O A:PRO21 4.9 20.2 1.0
CG A:GLU22 4.9 25.4 1.0
N A:THR7 4.9 26.4 1.0
CG A:PRO6 4.9 31.6 1.0

Chlorine binding site 2 out of 5 in 5r9l

Go back to Chlorine Binding Sites List in 5r9l
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:32.6
occ:1.00
 N A:ASN100 3.2 25.9 1.0
N A:ASP101 3.3 25.3 1.0
OG1 A:THR91 3.4 22.6 1.0
CB A:ALA93 3.7 26.0 1.0
O A:GLU98 3.7 34.5 1.0
N A:ALA93 3.8 24.3 1.0
CA A:ASN100 3.9 28.8 1.0
CG A:PRO92 4.0 28.1 1.0
CB A:ASP101 4.0 25.8 1.0
C A:ASN100 4.0 29.2 1.0
CD A:PRO92 4.1 24.1 1.0
CB A:ASN100 4.1 32.5 1.0
CA A:ALA93 4.1 25.3 1.0
CA A:ASP101 4.1 24.9 1.0
O A:ASP101 4.2 23.5 1.0
C A:PHE99 4.2 30.5 1.0
CA A:PHE99 4.2 27.4 1.0
OD2 A:ASP101 4.5 33.5 1.0
CG A:ASP101 4.5 33.6 1.0
ND2 A:ASN100 4.5 42.4 1.0
N A:PRO92 4.5 21.6 1.0
C A:PRO92 4.6 26.0 1.0
C A:ASP101 4.6 20.5 1.0
C A:GLU98 4.7 33.6 1.0
CG A:ASN100 4.8 39.6 1.0
CD1 A:PHE99 4.8 23.4 1.0
CB A:THR91 4.8 21.5 1.0
CB A:PRO92 4.9 27.1 1.0
CA A:PRO92 4.9 22.6 1.0
N A:PHE99 5.0 30.9 1.0

Chlorine binding site 3 out of 5 in 5r9l

Go back to Chlorine Binding Sites List in 5r9l
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:25.3
occ:0.55
 O A:HOH569 2.9 30.7 1.0
N A:ASP324 3.0 20.0 1.0
CB A:ASP324 3.5 20.9 1.0
NH2 A:ARG73 3.6 21.5 1.0
O A:PRO322 3.7 21.8 1.0
CA A:TYR323 3.8 18.9 1.0
CA A:ASP324 3.8 20.3 1.0
C A:TYR323 3.9 21.5 1.0
CD1 A:TYR323 4.4 23.0 1.0
O A:ASP324 4.4 22.2 1.0
O A:HOH756 4.4 40.0 1.0
C A:PRO322 4.5 21.3 1.0
N A:TYR323 4.5 20.2 1.0
O A:HOH778 4.6 24.3 1.0
O A:HOH534 4.6 27.9 1.0
C A:ASP324 4.6 21.8 1.0
CZ A:ARG73 4.7 21.8 1.0
CE1 A:HIS77 4.8 24.0 1.0
ND1 A:HIS77 4.8 25.3 1.0
CB A:TYR323 4.9 21.2 1.0
CG A:ASP324 4.9 23.9 1.0
CG A:TYR323 4.9 19.6 1.0

Chlorine binding site 4 out of 5 in 5r9l

Go back to Chlorine Binding Sites List in 5r9l
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:26.7
occ:0.79
 O A:HOH625 3.0 32.1 1.0
OG A:SER154 3.2 20.9 1.0
N A:SER154 3.3 18.4 1.0
O A:HOH718 3.4 37.5 1.0
CB A:SER154 3.5 18.9 1.0
CD A:PRO153 3.7 18.7 1.0
N A:PRO153 3.8 16.7 1.0
CG A:LYS152 3.9 19.8 1.0
ND2 A:ASN114 3.9 33.3 1.0
CB A:LYS152 4.0 18.8 1.0
CD A:LYS152 4.0 21.3 1.0
CA A:SER154 4.0 20.1 1.0
CB A:PRO153 4.2 18.8 1.0
C A:PRO153 4.2 20.1 1.0
CA A:PRO153 4.3 17.6 1.0
C A:LYS152 4.4 17.8 1.0
CG A:PRO153 4.4 17.8 1.0
CB A:ALA184 4.4 22.6 1.0
CE1 A:TYR188 4.4 17.1 1.0
CE A:LYS152 4.7 22.1 1.0
CA A:LYS152 4.8 17.4 1.0
CG A:ASN114 4.9 36.2 1.0
OH A:TYR188 4.9 18.9 1.0
OD1 A:ASN114 4.9 38.9 1.0
CZ A:TYR188 4.9 17.9 1.0

Chlorine binding site 5 out of 5 in 5r9l

Go back to Chlorine Binding Sites List in 5r9l
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14274A 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 N14274A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:36.7
occ:0.65
 N A:GLN264 3.2 23.9 1.0
CA A:ALA263 3.7 24.7 1.0
CB A:ALA263 3.9 26.5 1.0
C A:ALA263 3.9 24.9 1.0
CG A:GLN264 4.0 31.5 1.0
CB A:GLN264 4.1 26.6 1.0
CA A:GLN264 4.2 22.7 1.0
NE2 A:GLN264 4.6 33.3 1.0
O A:GLN264 4.8 25.6 1.0
CD A:GLN264 4.8 35.1 1.0
N A:ALA263 4.9 25.4 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 16:06:55 2024

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