Fluorine in PDB 7ore: Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4)

Enzymatic activity of Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4)

All present enzymatic activity of Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4):
2.7.11.24;

Protein crystallography data

The structure of Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4), PDB code: 7ore was solved by A.Chaikuad, M.Reynders, D.Trauner, S.Knapp, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.65 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.868, 71.059, 107.456, 90, 90, 90
R / Rfree (%) 21.6 / 27.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4) (pdb code 7ore). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4), PDB code: 7ore:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7ore

Go back to Fluorine Binding Sites List in 7ore
Fluorine binding site 1 out of 3 in the Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:41.3
occ:0.50
 F A:0EI501 0.0 41.3 0.5
F A:0EI502 0.1 48.1 0.2
F A:0EI502 0.1 40.3 0.3
C23 A:0EI502 1.3 40.2 0.3
C23 A:0EI501 1.4 41.1 0.5
C23 A:0EI502 1.4 48.0 0.2
C24 A:0EI502 2.3 39.7 0.3
C22 A:0EI502 2.3 48.3 0.2
C24 A:0EI501 2.3 41.5 0.5
C22 A:0EI501 2.3 40.3 0.5
C22 A:0EI502 2.4 40.4 0.3
C24 A:0EI502 2.4 47.7 0.2
C A:LEU144 3.2 36.8 1.0
O A:LEU144 3.3 38.8 1.0
CB A:LEU144 3.3 37.4 1.0
N A:VAL145 3.4 36.5 1.0
C A:VAL145 3.5 37.5 1.0
N A:MET146 3.5 38.5 1.0
C25 A:0EI502 3.6 39.9 0.3
C25 A:0EI501 3.6 41.7 0.5
C21 A:0EI501 3.6 40.7 0.5
C21 A:0EI502 3.6 48.6 0.2
C21 A:0EI502 3.6 40.5 0.3
C25 A:0EI502 3.6 48.0 0.2
CA A:VAL145 3.7 37.4 1.0
CG A:MET146 3.8 40.7 1.0
CB A:MET146 3.8 40.1 1.0
CA A:LEU144 3.9 36.7 1.0
O A:VAL145 3.9 35.7 1.0
CD2 A:LEU126 4.0 45.5 1.0
C20 A:0EI502 4.1 40.2 0.3
C20 A:0EI501 4.1 41.4 0.5
C20 A:0EI502 4.1 48.4 0.2
O A:ALA91 4.2 34.6 1.0
SD A:MET146 4.2 43.8 1.0
CA A:MET146 4.3 39.6 1.0
CD1 A:ILE124 4.6 40.3 1.0
CB A:LYS93 4.6 46.2 1.0
CG A:LEU144 4.7 38.4 1.0
N A:LYS93 4.7 39.1 1.0
CD1 A:LEU144 4.9 40.1 1.0

Fluorine binding site 2 out of 3 in 7ore

Go back to Fluorine Binding Sites List in 7ore
Fluorine binding site 2 out of 3 in the Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:40.3
occ:0.30
 F A:0EI502 0.0 40.3 0.3
F A:0EI501 0.1 41.3 0.5
F A:0EI502 0.2 48.1 0.2
C23 A:0EI502 1.4 40.2 0.3
C23 A:0EI501 1.4 41.1 0.5
C23 A:0EI502 1.4 48.0 0.2
C22 A:0EI502 2.3 48.3 0.2
C24 A:0EI501 2.3 41.5 0.5
C22 A:0EI502 2.3 40.4 0.3
C24 A:0EI502 2.3 39.7 0.3
C22 A:0EI501 2.4 40.3 0.5
C24 A:0EI502 2.5 47.7 0.2
C A:LEU144 3.2 36.8 1.0
CB A:LEU144 3.3 37.4 1.0
O A:LEU144 3.4 38.8 1.0
N A:VAL145 3.4 36.5 1.0
C A:VAL145 3.5 37.5 1.0
N A:MET146 3.6 38.5 1.0
C25 A:0EI501 3.6 41.7 0.5
C21 A:0EI502 3.6 48.6 0.2
C21 A:0EI502 3.6 40.5 0.3
C25 A:0EI502 3.6 39.9 0.3
C21 A:0EI501 3.7 40.7 0.5
C25 A:0EI502 3.7 48.0 0.2
CB A:MET146 3.8 40.1 1.0
CG A:MET146 3.8 40.7 1.0
CA A:VAL145 3.8 37.4 1.0
CA A:LEU144 3.9 36.7 1.0
O A:VAL145 3.9 35.7 1.0
CD2 A:LEU126 3.9 45.5 1.0
C20 A:0EI502 4.1 40.2 0.3
C20 A:0EI501 4.1 41.4 0.5
C20 A:0EI502 4.2 48.4 0.2
SD A:MET146 4.2 43.8 1.0
CA A:MET146 4.3 39.6 1.0
O A:ALA91 4.3 34.6 1.0
CD1 A:ILE124 4.5 40.3 1.0
CB A:LYS93 4.6 46.2 1.0
CG A:LEU144 4.6 38.4 1.0
N A:LYS93 4.8 39.1 1.0
CD1 A:LEU144 4.8 40.1 1.0

Fluorine binding site 3 out of 3 in 7ore

Go back to Fluorine Binding Sites List in 7ore
Fluorine binding site 3 out of 3 in the Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of JNK3 in Complex with Light-Activated Covalent Inhibitor Mr-II-249 with Both Non-Covalent and Covalent Binding Modes (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:48.1
occ:0.20
 F A:0EI502 0.0 48.1 0.2
F A:0EI501 0.1 41.3 0.5
F A:0EI502 0.2 40.3 0.3
C23 A:0EI502 1.3 40.2 0.3
C23 A:0EI501 1.3 41.1 0.5
C23 A:0EI502 1.4 48.0 0.2
C24 A:0EI502 2.2 39.7 0.3
C22 A:0EI501 2.3 40.3 0.5
C22 A:0EI502 2.3 48.3 0.2
C24 A:0EI502 2.3 47.7 0.2
C24 A:0EI501 2.4 41.5 0.5
C22 A:0EI502 2.4 40.4 0.3
C A:LEU144 3.2 36.8 1.0
O A:LEU144 3.3 38.8 1.0
CB A:LEU144 3.4 37.4 1.0
N A:VAL145 3.4 36.5 1.0
C A:VAL145 3.4 37.5 1.0
N A:MET146 3.5 38.5 1.0
C25 A:0EI502 3.5 39.9 0.3
C21 A:0EI501 3.6 40.7 0.5
C25 A:0EI501 3.6 41.7 0.5
C21 A:0EI502 3.6 48.6 0.2
C25 A:0EI502 3.6 48.0 0.2
C21 A:0EI502 3.6 40.5 0.3
CA A:VAL145 3.7 37.4 1.0
CG A:MET146 3.7 40.7 1.0
CB A:MET146 3.7 40.1 1.0
O A:VAL145 3.9 35.7 1.0
CA A:LEU144 3.9 36.7 1.0
CD2 A:LEU126 4.0 45.5 1.0
C20 A:0EI502 4.1 40.2 0.3
C20 A:0EI501 4.1 41.4 0.5
C20 A:0EI502 4.1 48.4 0.2
O A:ALA91 4.2 34.6 1.0
SD A:MET146 4.2 43.8 1.0
CA A:MET146 4.2 39.6 1.0
CB A:LYS93 4.6 46.2 1.0
CD1 A:ILE124 4.6 40.3 1.0
N A:LYS93 4.7 39.1 1.0
CG A:LEU144 4.7 38.4 1.0
CD1 A:LEU144 4.9 40.1 1.0
C A:ALA91 5.0 36.3 1.0

Reference:

M.Reynders, A.Chaikuad, B.T.Berger, K.Bauer, P.Koch, S.Laufer, S.Knapp, D.Trauner. Controlling the Covalent Reactivity of A Kinase Inhibitor with Light. Angew Chem Int Ed Engl 2021.
ISSN: ESSN 1521-3773
PubMed: 34081840
DOI: 10.1002/ANIE.202103767
Page generated: Fri Aug 2 10:48:23 2024

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