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Fluorine in PDB 5ra8: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha, PDB code: 5ra8 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) 29.73 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.887, 86.638, 126.501, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21

Other elements in 5ra8:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha (pdb code 5ra8). 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 N05711B in Complex with Map Kinase P38-Alpha, PDB code: 5ra8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5ra8

Go back to Fluorine Binding Sites List in 5ra8
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.2
occ:0.50
 F1 A:2O6401 0.0 30.2 0.5
C7 A:2O6401 1.4 28.1 0.5
F2 A:2O6401 2.1 26.8 0.5
F3 A:2O6401 2.2 27.0 0.5
C1 A:2O6401 2.4 27.7 0.5
C2 A:2O6401 2.8 29.4 0.5
OG1 A:THR106 3.0 26.6 1.0
C6 A:2O6401 3.6 28.3 0.5
CB A:ALA51 3.7 25.6 1.0
CG2 A:THR106 3.8 26.6 1.0
CB A:THR106 4.1 26.1 1.0
O A:ALA51 4.1 21.6 1.0
C3 A:2O6401 4.2 29.9 0.5
C A:ALA51 4.4 21.6 1.0
CB A:LYS53 4.4 24.3 0.5
N A:THR106 4.6 21.9 1.0
CA A:ALA51 4.7 22.8 1.0
C5 A:2O6401 4.8 28.1 0.5
CG1 A:VAL38 4.8 22.0 0.5
O A:LEU104 4.8 22.9 1.0
N A:LYS53 4.9 23.1 0.5
CA A:THR106 4.9 22.6 1.0
C4 A:2O6401 5.0 29.4 0.5
CG2 A:VAL38 5.0 21.2 0.5

Fluorine binding site 2 out of 3 in 5ra8

Go back to Fluorine Binding Sites List in 5ra8
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:26.8
occ:0.50
 F2 A:2O6401 0.0 26.8 0.5
C7 A:2O6401 1.4 28.1 0.5
F1 A:2O6401 2.1 30.2 0.5
F3 A:2O6401 2.1 27.0 0.5
C1 A:2O6401 2.4 27.7 0.5
C2 A:2O6401 3.2 29.4 0.5
C6 A:2O6401 3.3 28.3 0.5
CB A:LYS53 3.4 24.3 0.5
CG2 A:VAL38 3.5 21.2 0.5
CD A:LYS53 3.7 25.6 0.5
CG A:LYS53 3.9 25.6 0.5
O A:TYR35 4.1 26.5 0.5
CB A:TYR35 4.2 28.9 0.5
CG1 A:VAL38 4.3 22.0 0.5
CA A:LYS53 4.5 23.8 0.5
C3 A:2O6401 4.5 29.9 0.5
C5 A:2O6401 4.5 28.1 0.5
CB A:VAL38 4.6 21.7 0.5
CE A:LYS53 4.7 26.7 0.5
C A:TYR35 4.7 27.8 0.5
N A:LYS53 4.7 23.1 0.5
C4 A:2O6401 4.9 29.4 0.5

Fluorine binding site 3 out of 3 in 5ra8

Go back to Fluorine Binding Sites List in 5ra8
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.0
occ:0.50
 F3 A:2O6401 0.0 27.0 0.5
C7 A:2O6401 1.3 28.1 0.5
F2 A:2O6401 2.1 26.8 0.5
F1 A:2O6401 2.2 30.2 0.5
C1 A:2O6401 2.4 27.7 0.5
C6 A:2O6401 2.8 28.3 0.5
CB A:LYS53 3.3 24.3 0.5
CD A:LYS53 3.6 25.6 0.5
C2 A:2O6401 3.6 29.4 0.5
CB A:LEU104 3.9 21.3 1.0
CG A:LYS53 4.0 25.6 0.5
C5 A:2O6401 4.1 28.1 0.5
O A:LEU104 4.2 22.9 1.0
CG2 A:THR106 4.2 26.6 1.0
CD1 A:LEU104 4.4 26.4 1.0
CA A:LYS53 4.5 23.8 0.5
OG1 A:THR106 4.6 26.6 1.0
N A:LYS53 4.6 23.1 0.5
C A:LEU104 4.6 21.4 1.0
C3 A:2O6401 4.8 29.9 0.5
CG A:LEU104 4.8 22.0 1.0
OE2 A:GLU71 4.9 31.9 1.0
CE A:LYS53 4.9 26.7 0.5
C4 A:2O6401 4.9 29.4 0.5
CA A:LEU104 4.9 21.0 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: Tue Jul 15 06:50:44 2025

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