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Fluorine in PDB 7aw4: Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library

Enzymatic activity of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library

All present enzymatic activity of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library:
2.7.10.1;

Protein crystallography data

The structure of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library, PDB code: 7aw4 was solved by A.Pflug, J.W.M.Nissink, C.Blackett, K.Goldberg, E.J.Hennessy, E.Hardaker, W.Mccoull, L.Mcmurray, O.Collingwood, R.Overman, M.Preston, P.Rawlins, E.Rivers, M.Schimpl, P.Smith, E.Underwood, C.Truman, J.Warwicker, J.Winter, S.Woodcock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.48 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.568, 90.49, 69.415, 90, 99.37, 90
R / Rfree (%) 21.4 / 24.6

Other elements in 7aw4:

The structure of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library (pdb code 7aw4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library, PDB code: 7aw4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7aw4

Go back to Fluorine Binding Sites List in 7aw4
Fluorine binding site 1 out of 6 in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:30.0
occ:1.00
 F2 A:S5E901 0.0 30.0 1.0
C28 A:S5E901 1.3 28.2 1.0
F1 A:S5E901 2.1 29.4 1.0
F A:S5E901 2.2 28.9 1.0
C25 A:S5E901 2.4 23.7 1.0
C26 A:S5E901 2.8 23.2 1.0
N A:ALA740 3.5 23.2 1.0
C A:VAL739 3.5 25.6 1.0
CA A:ALA740 3.5 23.4 1.0
CD2 A:HIS721 3.5 28.6 1.0
O A:VAL739 3.6 24.0 1.0
C24 A:S5E901 3.6 21.4 1.0
NE2 A:HIS721 3.6 28.2 1.0
CG2 A:VAL739 3.7 25.6 1.0
C A:ALA740 3.7 28.7 1.0
CB A:VAL739 3.9 25.8 1.0
O A:ALA740 3.9 27.9 1.0
CD1 A:LEU714 4.1 26.9 1.0
C27 A:S5E901 4.2 23.6 1.0
CA A:VAL739 4.3 22.2 1.0
N A:ASP741 4.3 26.3 1.0
CG A:HIS721 4.5 27.3 1.0
CE1 A:HIS721 4.6 27.6 1.0
C23 A:S5E901 4.7 22.4 1.0
N1 A:S5E901 4.8 29.8 1.0
CG1 A:VAL649 4.9 22.9 1.0
CB A:ALA740 5.0 24.0 1.0
C22 A:S5E901 5.0 23.6 1.0
CG2 A:ILE650 5.0 22.9 1.0

Fluorine binding site 2 out of 6 in 7aw4

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Fluorine binding site 2 out of 6 in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:28.9
occ:1.00
 F A:S5E901 0.0 28.9 1.0
C28 A:S5E901 1.3 28.2 1.0
F1 A:S5E901 2.1 29.4 1.0
F2 A:S5E901 2.2 30.0 1.0
C25 A:S5E901 2.4 23.7 1.0
C24 A:S5E901 2.8 21.4 1.0
N1 A:S5E901 3.1 29.8 1.0
C5 A:S5E901 3.4 29.8 1.0
C6 A:S5E901 3.4 26.7 1.0
C26 A:S5E901 3.6 23.2 1.0
CG2 A:ILE650 3.7 22.9 1.0
N2 A:S5E901 3.9 28.6 1.0
CA A:ALA740 3.9 23.4 1.0
O A:VAL739 3.9 24.0 1.0
C23 A:S5E901 4.1 22.4 1.0
C A:ALA740 4.4 28.7 1.0
CG1 A:VAL649 4.4 22.9 1.0
C4 A:S5E901 4.4 30.1 1.0
C A:VAL739 4.4 25.6 1.0
N A:ALA740 4.4 23.2 1.0
N A:ASP741 4.5 26.3 1.0
O A:ILE650 4.6 21.6 1.0
SD A:MET641 4.6 47.8 1.0
C27 A:S5E901 4.7 23.6 1.0
N A:ILE650 4.8 20.0 1.0
S A:S5E901 4.9 28.9 1.0
CB A:ILE650 4.9 22.7 1.0
C22 A:S5E901 5.0 23.6 1.0
CB A:ALA740 5.0 24.0 1.0

Fluorine binding site 3 out of 6 in 7aw4

Go back to Fluorine Binding Sites List in 7aw4
Fluorine binding site 3 out of 6 in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:29.4
occ:1.00
 F1 A:S5E901 0.0 29.4 1.0
C28 A:S5E901 1.3 28.2 1.0
F A:S5E901 2.1 28.9 1.0
F2 A:S5E901 2.1 30.0 1.0
C25 A:S5E901 2.3 23.7 1.0
C24 A:S5E901 3.2 21.4 1.0
C26 A:S5E901 3.2 23.2 1.0
CD1 A:LEU714 3.4 26.9 1.0
CD2 A:LEU714 3.6 27.8 1.0
CG1 A:VAL649 3.9 22.9 1.0
CG A:LEU714 4.1 26.9 1.0
CE1 A:PHE719 4.2 35.0 1.0
SD A:MET641 4.3 47.8 1.0
C23 A:S5E901 4.4 22.4 1.0
C27 A:S5E901 4.4 23.6 1.0
CG2 A:VAL739 4.5 25.6 1.0
CD1 A:PHE719 4.6 34.2 1.0
CZ A:PHE719 4.8 34.3 1.0
O A:VAL739 4.8 24.0 1.0
CD2 A:HIS721 4.9 28.6 1.0
C22 A:S5E901 5.0 23.6 1.0
C6 A:S5E901 5.0 26.7 1.0

Fluorine binding site 4 out of 6 in 7aw4

Go back to Fluorine Binding Sites List in 7aw4
Fluorine binding site 4 out of 6 in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:36.9
occ:1.00
 F2 B:S5E901 0.0 36.9 1.0
C28 B:S5E901 1.3 36.4 1.0
F1 B:S5E901 2.1 38.1 1.0
F B:S5E901 2.1 38.8 1.0
C25 B:S5E901 2.3 33.3 1.0
C26 B:S5E901 2.8 31.1 1.0
CA B:ALA740 3.3 29.7 1.0
N B:ALA740 3.3 29.0 1.0
C B:ALA740 3.4 35.9 1.0
C B:VAL739 3.5 30.7 1.0
NE2 B:HIS721 3.5 27.6 1.0
C24 B:S5E901 3.5 33.8 1.0
CD2 B:HIS721 3.6 28.2 1.0
O B:VAL739 3.6 29.8 1.0
O B:ALA740 3.7 34.7 1.0
CG2 B:VAL739 3.9 28.1 1.0
N B:ASP741 4.0 35.0 1.0
CB B:VAL739 4.1 28.6 1.0
C27 B:S5E901 4.2 31.6 1.0
CA B:VAL739 4.4 26.0 1.0
CD1 B:LEU714 4.4 31.4 1.0
CE1 B:HIS721 4.4 27.2 1.0
CG B:HIS721 4.5 26.9 1.0
C23 B:S5E901 4.7 34.3 1.0
N1 B:S5E901 4.7 40.4 1.0
CB B:ALA740 4.7 30.2 1.0
CB B:ASP741 4.8 39.1 1.0
CG2 B:ILE650 4.9 30.2 1.0
CA B:ASP741 4.9 36.7 1.0
C22 B:S5E901 5.0 33.9 1.0
N2 B:S5E901 5.0 39.4 1.0

Fluorine binding site 5 out of 6 in 7aw4

Go back to Fluorine Binding Sites List in 7aw4
Fluorine binding site 5 out of 6 in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:38.8
occ:1.00
 F B:S5E901 0.0 38.8 1.0
C28 B:S5E901 1.3 36.4 1.0
F1 B:S5E901 2.1 38.1 1.0
F2 B:S5E901 2.1 36.9 1.0
C25 B:S5E901 2.4 33.3 1.0
C24 B:S5E901 2.8 33.8 1.0
N1 B:S5E901 3.1 40.4 1.0
C5 B:S5E901 3.6 40.9 1.0
CE B:MET641 3.6 54.5 1.0
C26 B:S5E901 3.6 31.1 1.0
C6 B:S5E901 3.6 39.7 1.0
CG2 B:ILE650 3.7 30.2 1.0
N2 B:S5E901 3.9 39.4 1.0
CA B:ALA740 3.9 29.7 1.0
O B:VAL739 4.0 29.8 1.0
C23 B:S5E901 4.1 34.3 1.0
C B:ALA740 4.3 35.9 1.0
N B:ASP741 4.4 35.0 1.0
N B:ALA740 4.4 29.0 1.0
C B:VAL739 4.5 30.7 1.0
CG1 B:VAL649 4.5 27.9 1.0
C4 B:S5E901 4.5 41.6 1.0
SD B:MET641 4.6 57.8 1.0
O B:ILE650 4.6 29.8 1.0
C27 B:S5E901 4.8 31.6 1.0
N B:ILE650 4.9 26.4 1.0
S B:S5E901 4.9 41.5 1.0
CB B:ILE650 4.9 29.1 1.0
CB B:ALA740 4.9 30.2 1.0
C22 B:S5E901 5.0 33.9 1.0

Fluorine binding site 6 out of 6 in 7aw4

Go back to Fluorine Binding Sites List in 7aw4
Fluorine binding site 6 out of 6 in the Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Mertk Kinase Domain with Type 3 Inhibitor From A Dna-Encoded Library within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:38.1
occ:1.00
 F1 B:S5E901 0.0 38.1 1.0
C28 B:S5E901 1.3 36.4 1.0
F2 B:S5E901 2.1 36.9 1.0
F B:S5E901 2.1 38.8 1.0
C25 B:S5E901 2.3 33.3 1.0
C26 B:S5E901 3.1 31.1 1.0
C24 B:S5E901 3.3 33.8 1.0
CE B:MET641 3.4 54.5 1.0
CD1 B:LEU714 3.4 31.4 1.0
CD2 B:LEU714 3.7 34.0 1.0
CG1 B:VAL649 4.1 27.9 1.0
CG B:LEU714 4.2 31.5 1.0
CE1 B:PHE719 4.3 38.6 1.0
C27 B:S5E901 4.4 31.6 1.0
CG2 B:VAL739 4.4 28.1 1.0
C23 B:S5E901 4.5 34.3 1.0
CD2 B:HIS721 4.7 28.2 1.0
O B:VAL739 4.7 29.8 1.0
CD1 B:PHE719 4.7 38.2 1.0
SD B:MET641 4.8 57.8 1.0
C22 B:S5E901 5.0 33.9 1.0

Reference:

J.W.M.Nissink, C.Blackett, M.Clarke, J.Disch, K.Goldberg, J.Guilinger, E.J.Hennessy, R.Jetson, D.Ginkunja, E.Hardaker, A.Keefe, W.Mccoull, L.Mcmurray, O.Collingwood, R.Overman, A.Pflug, M.Preston, P.Rawlins, E.Rivers, M.Schimpl, P.Smith, E.Underwood, C.Truman, J.Warwicker, J.Winter, S.Woodcock, Y.Zhang. Generating Selective Leads For Mer Kinase Inhibitors - Example of A Comprehensive Lead-Generation Strategy J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
Page generated: Fri Aug 2 05:47:00 2024

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