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Fluorine in PDB 6yoj: Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One

Enzymatic activity of Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One

All present enzymatic activity of Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One:
2.7.10.2;

Protein crystallography data

The structure of Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One, PDB code: 6yoj was solved by D.Musil, T.Heinrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.33 / 1.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.525, 48.396, 129.325, 90, 90, 90
R / Rfree (%) 17.1 / 19.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One (pdb code 6yoj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One, PDB code: 6yoj:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6yoj

Go back to Fluorine Binding Sites List in 6yoj
Fluorine binding site 1 out of 3 in the Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:9.8
occ:1.00
 F20 A:P4N701 0.0 9.8 1.0
C19 A:P4N701 1.4 9.4 1.0
F21 A:P4N701 2.2 9.7 1.0
F22 A:P4N701 2.3 9.9 1.0
C18 A:P4N701 2.4 7.4 1.0
N12 A:P4N701 2.9 8.4 1.0
C13 A:P4N701 3.0 7.7 1.0
CB A:ALA452 3.4 9.8 1.0
C17 A:P4N701 3.5 7.7 1.0
CB A:MET499 3.7 8.9 1.0
CG A:MET499 3.7 9.9 1.0
CD1 A:LEU567 3.8 9.6 1.0
N14 A:P4N701 4.3 6.9 1.0
CG1 A:VAL436 4.3 10.7 1.0
C11 A:P4N701 4.3 7.8 1.0
CG A:LYS454 4.4 9.1 1.0
CB A:ASP564 4.5 8.3 1.0
CD A:LYS454 4.5 8.5 1.0
N16 A:P4N701 4.6 7.5 1.0
CA A:ALA452 4.7 9.4 1.0
C A:ALA452 4.9 10.0 1.0
O A:GLU500 4.9 11.1 1.0
C15 A:P4N701 4.9 7.6 1.0
C4 A:P4N701 5.0 8.3 1.0
O A:ALA452 5.0 11.4 1.0

Fluorine binding site 2 out of 3 in 6yoj

Go back to Fluorine Binding Sites List in 6yoj
Fluorine binding site 2 out of 3 in the Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:9.7
occ:1.00
 F21 A:P4N701 0.0 9.7 1.0
C19 A:P4N701 1.4 9.4 1.0
F22 A:P4N701 2.2 9.9 1.0
F20 A:P4N701 2.2 9.8 1.0
C18 A:P4N701 2.4 7.4 1.0
C13 A:P4N701 3.0 7.7 1.0
N12 A:P4N701 3.0 8.4 1.0
CB A:ASP564 3.3 8.3 1.0
O9 A:P4N701 3.4 9.7 1.0
C17 A:P4N701 3.4 7.7 1.0
CD1 A:LEU567 3.6 9.6 1.0
N A:ASP564 3.6 7.4 1.0
C4 A:P4N701 3.7 8.3 1.0
CD1 A:LEU553 3.9 8.6 1.0
CA A:ASP564 4.1 7.4 1.0
N14 A:P4N701 4.2 6.9 1.0
C11 A:P4N701 4.3 7.8 1.0
C5 A:P4N701 4.5 8.1 1.0
N16 A:P4N701 4.5 7.5 1.0
CG A:ASP564 4.5 10.4 1.0
CG1 A:VAL484 4.5 11.0 0.5
S7 A:P4N701 4.6 8.3 1.0
C3 A:P4N701 4.6 8.0 1.0
CG2 A:VAL484 4.6 9.3 0.5
C A:GLY563 4.7 7.5 1.0
CG A:LEU567 4.8 9.8 1.0
C15 A:P4N701 4.8 7.6 1.0
CA A:GLY563 4.9 7.1 1.0
CG2 A:VAL484 4.9 11.0 0.5

Fluorine binding site 3 out of 3 in 6yoj

Go back to Fluorine Binding Sites List in 6yoj
Fluorine binding site 3 out of 3 in the Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Focal Adhesion Kinase Catalytic Domain in Complex with 6-[4-(3- Methanesulfonyl-Benzylamino)-5-Trifluoromethyl-Pyrimidin-2-Ylamino]- 3,4-Dihydro-1H-Quinolin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:9.9
occ:1.00
 F22 A:P4N701 0.0 9.9 1.0
C19 A:P4N701 1.4 9.4 1.0
F21 A:P4N701 2.2 9.7 1.0
F20 A:P4N701 2.3 9.8 1.0
C18 A:P4N701 2.4 7.4 1.0
C17 A:P4N701 2.7 7.7 1.0
CB A:MET499 3.2 8.9 1.0
CG2 A:VAL484 3.3 11.0 0.5
O A:GLU500 3.5 11.1 1.0
C13 A:P4N701 3.7 7.7 1.0
CG A:MET499 3.7 9.9 1.0
CG1 A:VAL484 3.8 11.0 0.5
CG2 A:VAL484 4.0 9.3 0.5
N16 A:P4N701 4.0 7.5 1.0
CE A:MET499 4.0 10.3 1.0
CB A:VAL484 4.1 8.8 0.5
CB A:VAL484 4.1 10.2 0.5
CG1 A:VAL484 4.2 9.3 0.5
N12 A:P4N701 4.3 8.4 1.0
CB A:ALA452 4.3 9.8 1.0
CB A:ASP564 4.4 8.3 1.0
CD1 A:LEU553 4.6 8.6 1.0
CA A:MET499 4.7 8.2 1.0
C A:GLU500 4.7 10.6 1.0
N14 A:P4N701 4.7 6.9 1.0
N A:ASP564 4.7 7.4 1.0
SD A:MET499 4.7 10.0 1.0
N A:GLU500 4.8 8.5 1.0
C15 A:P4N701 4.8 7.6 1.0
C A:MET499 4.8 8.8 1.0

Reference:

B.T.Berger, M.Amaral, D.B.Kokh, A.Nunes-Alves, D.Musil, T.Heinrich, M.Schroder, R.Neil, J.Wang, I.Navratilova, J.Bomke, J.M.Elkins, S.Muller, M.Frech, R.C.Wade, S.Knapp. Structure-Kinetic Relationship Reveals the Mechanism of Selectivity of Fak Inhibitors Over PYK2. Cell Chem Biol 2021.
ISSN: ESSN 2451-9456
PubMed: 33497606
DOI: 10.1016/J.CHEMBIOL.2021.01.003
Page generated: Fri Aug 2 04:45:32 2024

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