Atomistry » Fluorine » PDB 5qtr-5rah » 5ra8
Atomistry »
  Fluorine »
    PDB 5qtr-5rah »
      5ra8 »

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: Thu Aug 1 13:42:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy