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Chlorine in PDB 5r9i: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha, PDB code: 5r9i 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) 29.52 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.853, 87.203, 125.501, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.3

Other elements in 5r9i:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Bromine (Br) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 in Complex with Map Kinase P38-Alpha (pdb code 5r9i). 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 TCJ795 in Complex with Map Kinase P38-Alpha, PDB code: 5r9i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r9i

Go back to Chlorine Binding Sites List in 5r9i
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:45.1
occ:1.00
 O A:HOH736 2.6 36.5 1.0
N A:ARG23 3.1 24.5 1.0
O A:HOH564 3.2 36.1 1.0
O A:HOH711 3.3 41.0 1.0
CB A:ARG23 3.6 31.7 1.0
N A:GLU22 3.6 27.6 1.0
CB A:PRO6 3.7 36.4 1.0
CB A:PRO21 3.8 28.4 1.0
CA A:ARG23 3.9 25.4 1.0
C A:GLU22 4.0 27.4 1.0
CB A:GLU22 4.1 26.3 1.0
CG A:ARG23 4.1 28.8 1.0
CA A:GLU22 4.1 26.7 1.0
C A:PRO21 4.1 27.2 1.0
CA A:PRO21 4.4 26.7 1.0
CD A:ARG23 4.4 30.1 1.0
O A:THR7 4.5 33.2 1.0
CA A:PRO6 4.7 36.3 1.0
O A:HOH671 4.8 35.8 1.0
CG A:PRO6 4.8 36.7 1.0
CG A:GLU22 4.8 32.3 1.0
O A:PRO21 4.9 22.5 1.0
N A:THR7 4.9 30.1 1.0

Chlorine binding site 2 out of 6 in 5r9i

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Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:47.7
occ:1.00
 N A:ASN100 3.3 37.0 1.0
N A:ASP101 3.3 35.5 1.0
OG1 A:THR91 3.4 30.5 1.0
CB A:ALA93 3.6 35.4 1.0
O A:GLU98 3.6 42.1 1.0
N A:ALA93 3.8 32.7 1.0
CB A:ASP101 3.9 34.6 1.0
CA A:ASN100 4.1 37.3 1.0
CD A:PRO92 4.1 31.3 1.0
CG A:PRO92 4.1 35.6 1.0
C A:ASN100 4.1 38.8 1.0
CA A:ALA93 4.1 37.0 1.0
CA A:ASP101 4.1 33.8 1.0
C A:PHE99 4.2 40.1 1.0
CA A:PHE99 4.2 38.6 1.0
CB A:ASN100 4.3 45.6 1.0
O A:ASP101 4.3 32.5 1.0
OD2 A:ASP101 4.5 47.3 1.0
CG A:ASP101 4.5 46.0 1.0
N A:PRO92 4.6 31.4 1.0
C A:GLU98 4.6 44.6 1.0
C A:PRO92 4.7 35.5 1.0
C A:ASP101 4.7 26.4 1.0
CB A:THR91 4.8 28.7 1.0
CD1 A:PHE99 4.8 29.0 1.0
N A:PHE99 4.9 40.8 1.0
CB A:PRO92 5.0 34.3 1.0

Chlorine binding site 3 out of 6 in 5r9i

Go back to Chlorine Binding Sites List in 5r9i
Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:44.8
occ:1.00
 N A:ASP324 3.0 27.3 1.0
O A:HOH507 3.1 37.1 1.0
NH2 A:ARG73 3.5 27.1 1.0
CB A:ASP324 3.6 27.9 1.0
CA A:TYR323 3.8 29.1 1.0
O A:PRO322 3.8 26.9 1.0
C A:TYR323 3.9 28.7 1.0
CA A:ASP324 3.9 27.1 1.0
CD1 A:TYR323 4.3 26.7 1.0
O A:HOH710 4.4 46.4 1.0
O A:ASP324 4.4 29.9 1.0
N A:TYR323 4.5 24.5 1.0
C A:PRO322 4.5 27.8 1.0
O A:HOH560 4.6 34.2 1.0
C A:ASP324 4.6 24.5 1.0
CE1 A:HIS77 4.7 30.1 1.0
ND1 A:HIS77 4.7 31.4 1.0
CZ A:ARG73 4.7 26.2 1.0
CB A:TYR323 4.8 26.8 1.0
CG A:TYR323 4.9 25.3 1.0

Chlorine binding site 4 out of 6 in 5r9i

Go back to Chlorine Binding Sites List in 5r9i
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.6
occ:0.79
 O A:HOH618 2.9 40.1 1.0
N A:SER154 3.3 23.9 1.0
OG A:SER154 3.3 27.6 1.0
O A:HOH696 3.5 43.0 1.0
CB A:SER154 3.6 25.1 1.0
CD A:PRO153 3.7 20.9 1.0
N A:PRO153 3.8 22.8 1.0
ND2 A:ASN114 3.8 34.8 1.0
CG A:LYS152 3.9 27.3 1.0
CB A:LYS152 4.0 25.6 1.0
CA A:SER154 4.0 28.2 1.0
CB A:PRO153 4.1 26.3 1.0
C A:PRO153 4.2 24.8 1.0
CD A:LYS152 4.2 29.4 1.0
CA A:PRO153 4.2 21.0 1.0
CG A:PRO153 4.3 22.7 1.0
C A:LYS152 4.4 22.9 1.0
CE1 A:TYR188 4.4 19.1 1.0
CB A:ALA184 4.4 31.2 1.0
OD1 A:ASN114 4.7 46.7 1.0
CG A:ASN114 4.7 45.0 1.0
OH A:TYR188 4.7 24.2 1.0
CA A:LYS152 4.8 23.1 1.0
CE A:LYS152 4.8 34.0 1.0
CZ A:TYR188 4.9 24.2 1.0
O A:HOH506 5.0 38.7 1.0

Chlorine binding site 5 out of 6 in 5r9i

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Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:39.5
occ:0.68
 N A:ASN269 3.0 19.3 1.0
CB A:ASN269 3.5 24.9 1.0
CA A:ASN269 3.8 25.0 1.0
CB A:MET268 3.8 22.4 1.0
O A:ASN269 3.9 19.7 1.0
CA A:MET268 4.0 20.8 1.0
C A:MET268 4.0 22.1 1.0
CE A:MET268 4.0 32.4 1.0
CG A:MET268 4.2 25.1 1.0
C A:ASN269 4.3 18.9 1.0
CB A:ASN272 4.4 22.8 1.0
ND2 A:ASN272 4.6 26.5 1.0
O A:HOH714 4.7 31.4 1.0
CG A:ASN269 4.9 28.2 1.0
SD A:MET268 5.0 30.7 1.0

Chlorine binding site 6 out of 6 in 5r9i

Go back to Chlorine Binding Sites List in 5r9i
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment TCJ795 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 TCJ795 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:45.5
occ:0.79
 O A:ALA144 3.4 25.7 1.0
N A:TYR323 3.5 24.5 1.0
C A:ALA144 3.7 30.2 1.0
CA A:PRO322 3.8 26.1 1.0
OD2 A:ASP145 3.9 50.8 1.0
O A:TYR323 3.9 29.1 1.0
CB A:PRO322 4.0 33.2 1.0
O A:HOH537 4.0 31.2 1.0
CA A:ALA144 4.1 26.9 1.0
C A:PRO322 4.2 27.8 1.0
CB A:ASP145 4.3 33.7 1.0
CG A:ASP145 4.3 44.1 1.0
CA A:TYR323 4.4 29.1 1.0
N A:ASP145 4.5 24.7 1.0
O A:SER143 4.5 29.4 1.0
C A:TYR323 4.5 28.7 1.0
O A:HOH719 4.7 39.7 1.0
CB A:TYR323 4.8 26.8 1.0
CB A:ALA144 4.9 28.1 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: Sat Jul 12 07:54:30 2025

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