Fluorine in PDB 8bzp: JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety

Enzymatic activity of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety

All present enzymatic activity of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety:
2.7.11.24;

Protein crystallography data

The structure of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety, PDB code: 8bzp was solved by J.Stahlecker, S.Vaas, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 1.86
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.797, 155.376, 43.96, 90, 90, 90
R / Rfree (%) 18.9 / 21.6

Other elements in 8bzp:

The structure of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety (pdb code 8bzp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety, PDB code: 8bzp:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8bzp

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Fluorine binding site 1 out of 4 in the JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:78.6
occ:0.50
 F1 A:SWM501 0.0 78.6 0.5
C2 A:SWM501 1.3 69.7 0.5
F2 A:SWM501 1.6 78.2 0.5
BR1 A:SWM501 1.7 90.8 0.5
C2 A:SWM501 1.8 68.3 0.5
F2 A:SWM501 2.1 74.2 0.5
C1 A:SWM501 2.3 61.5 0.5
C1 A:SWM501 2.6 60.7 0.5
O1 A:SWM501 2.6 61.2 0.5
BR1 A:SWM501 2.7 93.7 0.5
O1 A:SWM501 2.7 57.6 0.5
F1 A:SWM501 3.0 75.7 0.5
O A:SER72 3.1 76.6 1.0
CA A:GLY73 3.4 75.9 1.0
C A:SER72 3.4 75.8 1.0
N1 A:SWM501 3.6 55.9 0.5
N A:GLY73 3.6 76.5 1.0
N1 A:SWM501 3.9 56.0 0.5
C A:GLY73 4.3 74.1 1.0
O A:GLY76 4.4 57.6 1.0
CA A:SER72 4.4 65.7 1.0
N A:SER72 4.6 56.9 1.0
C3 A:SWM501 4.8 54.9 0.5
N A:ALA74 4.8 79.5 1.0
O A:GLY73 5.0 72.3 1.0
N A:GLY76 5.0 62.6 1.0
N A:GLN75 5.0 66.9 1.0

Fluorine binding site 2 out of 4 in 8bzp

Go back to Fluorine Binding Sites List in 8bzp
Fluorine binding site 2 out of 4 in the JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:75.7
occ:0.50
 F1 A:SWM501 0.0 75.7 0.5
BR1 A:SWM501 1.2 93.7 0.5
C2 A:SWM501 1.3 68.3 0.5
C2 A:SWM501 1.8 69.7 0.5
F2 A:SWM501 2.1 78.2 0.5
C1 A:SWM501 2.3 61.5 0.5
N1 A:SWM501 2.3 55.9 0.5
C1 A:SWM501 2.3 60.7 0.5
F2 A:SWM501 2.3 74.2 0.5
N1 A:SWM501 2.6 56.0 0.5
BR1 A:SWM501 2.7 90.8 0.5
O A:HOH748 2.8 58.3 1.0
NZ A:LYS93 2.8 61.0 1.0
F1 A:SWM501 3.0 78.6 0.5
O1 A:SWM501 3.4 61.2 0.5
O1 A:SWM501 3.5 57.6 0.5
C3 A:SWM501 3.6 54.9 0.5
CE A:LYS93 3.9 56.7 1.0
CB A:GLN75 3.9 72.8 1.0
C3 A:SWM501 3.9 54.2 0.5
N2 A:SWM501 4.2 50.0 0.5
N2 A:SWM501 4.5 49.2 0.5
CD A:LYS93 4.7 47.0 1.0
O A:HOH735 4.9 58.0 1.0

Fluorine binding site 3 out of 4 in 8bzp

Go back to Fluorine Binding Sites List in 8bzp
Fluorine binding site 3 out of 4 in the JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:74.2
occ:0.50
 F2 A:SWM501 0.0 74.2 0.5
BR1 A:SWM501 0.7 90.8 0.5
C2 A:SWM501 1.3 69.7 0.5
C2 A:SWM501 1.7 68.3 0.5
F1 A:SWM501 2.1 78.6 0.5
C1 A:SWM501 2.3 61.5 0.5
F1 A:SWM501 2.3 75.7 0.5
C1 A:SWM501 2.4 60.7 0.5
BR1 A:SWM501 2.7 93.7 0.5
F2 A:SWM501 2.8 78.2 0.5
N1 A:SWM501 2.8 55.9 0.5
O1 A:SWM501 3.1 57.6 0.5
N1 A:SWM501 3.1 56.0 0.5
O1 A:SWM501 3.3 61.2 0.5
NZ A:LYS93 3.4 61.0 1.0
CE A:LYS93 3.4 56.7 1.0
O A:GLY76 3.7 57.6 1.0
N A:GLY76 3.7 62.6 1.0
CB A:GLN75 3.9 72.8 1.0
C3 A:SWM501 4.0 54.9 0.5
C A:GLY76 4.0 59.1 1.0
CG2 A:VAL78 4.1 43.9 1.0
CA A:GLY76 4.2 57.0 1.0
CD A:LYS93 4.2 47.0 1.0
C3 A:SWM501 4.3 54.2 0.5
C A:GLN75 4.3 65.0 1.0
N A:GLY73 4.4 76.5 1.0
CA A:GLN75 4.5 66.0 1.0
CA A:GLY73 4.5 75.9 1.0
N A:GLN75 4.5 66.9 1.0
C A:SER72 4.6 75.8 1.0
O A:SER72 4.7 76.6 1.0
N2 A:SWM501 4.8 50.0 0.5
CG A:LYS93 4.8 38.5 1.0
C A:GLY73 4.8 74.1 1.0
N A:ILE77 4.9 48.6 1.0

Fluorine binding site 4 out of 4 in 8bzp

Go back to Fluorine Binding Sites List in 8bzp
Fluorine binding site 4 out of 4 in the JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of JNK3 (Mitogen-Activated Protein Kinase 10) in Complex with Compound 23 Bearing A C(SP3)F2BR Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:78.2
occ:0.50
 F2 A:SWM501 0.0 78.2 0.5
C2 A:SWM501 1.3 68.3 0.5
C2 A:SWM501 1.5 69.7 0.5
F1 A:SWM501 1.6 78.6 0.5
BR1 A:SWM501 1.8 93.7 0.5
C1 A:SWM501 2.1 61.5 0.5
F1 A:SWM501 2.1 75.7 0.5
C1 A:SWM501 2.3 60.7 0.5
O1 A:SWM501 2.5 61.2 0.5
BR1 A:SWM501 2.7 90.8 0.5
F2 A:SWM501 2.8 74.2 0.5
O1 A:SWM501 2.8 57.6 0.5
N1 A:SWM501 3.1 55.9 0.5
N1 A:SWM501 3.4 56.0 0.5
O A:HOH748 4.1 58.3 1.0
C3 A:SWM501 4.4 54.9 0.5
O A:SER72 4.4 76.6 1.0
C3 A:SWM501 4.7 54.2 0.5
CA A:GLY73 4.7 75.9 1.0
OD1 A:ASN194 4.8 65.3 1.0
NZ A:LYS93 4.9 61.0 1.0
C A:SER72 4.9 75.8 1.0

Reference:

S.Vaas, M.O.Zimmermann, D.Schollmeyer, J.Stahlecker, M.U.Engelhardt, J.Rheinganz, B.Drotleff, M.Olfert, M.Lammerhofer, M.Kramer, T.Stehle, F.M.Boeckler. Principles and Applications of Cf 2 X Moieties As Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37487500
DOI: 10.1021/ACS.JMEDCHEM.3C00634
Page generated: Fri Aug 2 16:59:59 2024

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