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Fluorine in PDB 5r9v: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha, PDB code: 5r9v 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) 29.34 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.842, 86.205, 127.628, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 19

Other elements in 5r9v:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha (pdb code 5r9v). 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 N13596A in Complex with Map Kinase P38-Alpha, PDB code: 5r9v:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5r9v

Go back to Fluorine Binding Sites List in 5r9v
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:31.8
occ:0.46
 F A:SSY401 0.0 31.8 0.5
C9 A:SSY401 1.3 33.5 0.5
F2 A:SSY401 2.1 37.5 0.5
F1 A:SSY401 2.1 38.2 0.5
C8 A:SSY401 2.5 30.6 0.5
N A:SSY401 2.7 24.4 0.5
CG A:LEU291 3.2 29.0 1.0
O A:HOH503 3.2 28.2 1.0
CD1 A:LEU291 3.2 24.6 1.0
O1 A:SSY401 3.6 30.8 0.5
CD2 A:LEU291 3.6 24.6 1.0
CB A:PRO191 3.9 21.8 1.0
CG A:PRO191 4.0 22.8 1.0
C6 A:SSY401 4.2 24.2 0.5
CB A:LEU291 4.5 23.3 1.0
N A:GLU192 4.7 17.5 0.5
CD2 A:LEU236 4.7 17.4 1.0
CD1 A:LEU232 4.8 18.7 1.0
C7 A:SSY401 4.8 23.4 0.5
O A:LEU291 4.9 23.7 1.0
CG A:PRO242 4.9 18.4 0.5
C A:PRO191 5.0 19.2 1.0

Fluorine binding site 2 out of 3 in 5r9v

Go back to Fluorine Binding Sites List in 5r9v
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.2
occ:0.46
 F1 A:SSY401 0.0 38.2 0.5
C9 A:SSY401 1.3 33.5 0.5
F A:SSY401 2.1 31.8 0.5
F2 A:SSY401 2.1 37.5 0.5
C8 A:SSY401 2.4 30.6 0.5
O1 A:SSY401 2.9 30.8 0.5
N A:SSY401 3.3 24.4 0.5
CZ3 A:TRP197 3.6 20.4 0.5
CE3 A:TRP197 3.7 20.6 0.5
CD1 A:LEU232 3.7 18.7 1.0
CB A:PRO191 3.8 21.8 1.0
C A:PRO191 4.3 19.2 1.0
O A:PRO191 4.3 23.7 1.0
N A:GLU192 4.4 17.5 0.5
CD1 A:ILE259 4.5 31.7 0.5
C6 A:SSY401 4.6 24.2 0.5
CA A:PRO191 4.6 20.0 1.0
O A:HOH503 4.7 28.2 1.0
CA A:GLU192 4.7 17.2 0.5
CG A:PRO191 4.7 22.8 1.0
CH2 A:TRP197 4.9 19.4 0.5
CD2 A:LEU232 4.9 21.2 1.0
CG A:LEU232 5.0 17.5 1.0
CG1 A:ILE259 5.0 31.3 0.5

Fluorine binding site 3 out of 3 in 5r9v

Go back to Fluorine Binding Sites List in 5r9v
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:37.5
occ:0.46
 F2 A:SSY401 0.0 37.5 0.5
C9 A:SSY401 1.4 33.5 0.5
F A:SSY401 2.1 31.8 0.5
F1 A:SSY401 2.1 38.2 0.5
C8 A:SSY401 2.5 30.6 0.5
O1 A:SSY401 2.9 30.8 0.5
CD1 A:ILE259 3.3 31.7 0.5
N A:SSY401 3.5 24.4 0.5
CG A:PRO242 3.6 18.4 0.5
CG1 A:ILE259 3.9 31.3 0.5
CD2 A:LEU291 4.0 24.6 1.0
CD A:PRO242 4.3 18.5 0.5
CG A:LEU291 4.4 29.0 1.0
CD2 A:LEU236 4.4 17.4 1.0
CD1 A:LEU232 4.5 18.7 1.0
CZ3 A:TRP197 4.6 20.4 0.5
CD1 A:LEU291 4.7 24.6 1.0
C6 A:SSY401 4.8 24.2 0.5
CE3 A:TRP197 4.9 20.6 0.5

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 06:50:39 2025

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