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Fluorine in PDB 5r98: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha, PDB code: 5r98 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) 29.26 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.846, 85.944, 127.136, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20

Other elements in 5r98:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha (pdb code 5r98). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha, PDB code: 5r98:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5r98

Go back to Fluorine Binding Sites List in 5r98
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:40.3
occ:0.82
 F A:SQG401 0.0 40.3 0.8
C9 A:SQG401 1.3 34.3 0.8
F2 A:SQG401 2.1 35.0 0.8
F1 A:SQG401 2.2 33.2 0.8
O1 A:SQG401 2.2 27.3 0.8
C2 A:SQG401 2.8 28.7 0.8
CD1 A:ILE259 3.0 37.1 1.0
C3 A:SQG401 3.0 29.0 0.8
CZ3 A:TRP197 3.3 27.8 1.0
CE3 A:TRP197 3.5 23.6 1.0
CG1 A:ILE259 3.6 34.0 1.0
C1 A:SQG401 4.0 30.0 0.8
C4 A:SQG401 4.3 28.3 0.8
CH2 A:TRP197 4.5 24.1 1.0
CD2 A:TRP197 4.9 26.0 1.0
CD1 A:ILE250 4.9 29.9 1.0
CD1 A:LEU232 4.9 29.1 1.0
CG A:PRO242 4.9 24.9 1.0
CB A:ILE259 5.0 28.9 1.0
CB A:ALA255 5.0 28.9 1.0

Fluorine binding site 2 out of 3 in 5r98

Go back to Fluorine Binding Sites List in 5r98
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.2
occ:0.82
 F1 A:SQG401 0.0 33.2 0.8
C9 A:SQG401 1.3 34.3 0.8
F A:SQG401 2.2 40.3 0.8
F2 A:SQG401 2.2 35.0 0.8
O1 A:SQG401 2.3 27.3 0.8
C2 A:SQG401 2.7 28.7 0.8
C1 A:SQG401 3.2 30.0 0.8
CG A:PRO242 3.5 24.9 1.0
CD2 A:LEU291 3.5 26.4 1.0
C3 A:SQG401 3.6 29.0 0.8
CG A:LEU291 3.7 30.0 1.0
CD1 A:LEU291 3.9 24.0 1.0
CD1 A:ILE259 4.2 37.1 1.0
C A:SQG401 4.3 26.1 0.8
CD A:PRO242 4.3 22.2 1.0
CD2 A:LEU236 4.5 21.6 1.0
CD1 A:ILE250 4.6 29.9 1.0
C4 A:SQG401 4.6 28.3 0.8
CB A:PRO242 4.7 24.4 1.0
CD2 A:LEU246 4.7 26.1 1.0
CG1 A:ILE259 4.8 34.0 1.0
C5 A:SQG401 4.9 27.0 0.8

Fluorine binding site 3 out of 3 in 5r98

Go back to Fluorine Binding Sites List in 5r98
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.0
occ:0.82
 F2 A:SQG401 0.0 35.0 0.8
C9 A:SQG401 1.3 34.3 0.8
F A:SQG401 2.1 40.3 0.8
F1 A:SQG401 2.2 33.2 0.8
O1 A:SQG401 2.2 27.3 0.8
CD1 A:LEU232 3.3 29.1 1.0
C2 A:SQG401 3.5 28.7 0.8
CD2 A:LEU236 3.8 21.6 1.0
CB A:PRO191 4.1 19.9 1.0
CD1 A:LEU291 4.1 24.0 1.0
CZ3 A:TRP197 4.3 27.8 1.0
C1 A:SQG401 4.3 30.0 0.8
C3 A:SQG401 4.3 29.0 0.8
CG A:LEU232 4.4 27.2 1.0
CD1 A:LEU236 4.6 22.8 1.0
CD2 A:LEU232 4.6 30.8 1.0
CG A:LEU236 4.6 19.0 1.0
CD2 A:LEU291 4.7 26.4 1.0
CD1 A:ILE259 4.7 37.1 1.0
CG A:LEU291 4.7 30.0 1.0
CE3 A:TRP197 4.8 23.6 1.0
CG A:PRO191 4.8 23.6 1.0
CG1 A:ILE259 4.9 34.0 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: Thu Aug 1 13:40:26 2024

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