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Fluorine in PDB 6yvy: Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide

Enzymatic activity of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide

All present enzymatic activity of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide:
2.7.10.2;

Protein crystallography data

The structure of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide, PDB code: 6yvy was solved by D.Musil, M.Amaral, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.49 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.974, 75.856, 172.64, 90, 102.66, 90
R / Rfree (%) 21.4 / 23.5

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide (pdb code 6yvy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide, PDB code: 6yvy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6yvy

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Fluorine binding site 1 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


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 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:27.2
occ:1.00
 F22 A:P1E701 0.0 27.2 1.0
C15 A:P1E701 1.3 26.3 1.0
F21 A:P1E701 2.1 26.6 1.0
F16 A:P1E701 2.1 28.9 1.0
C12 A:P1E701 2.4 23.2 1.0
C11 A:P1E701 3.1 22.2 1.0
N8 A:P1E701 3.2 22.3 1.0
CE A:LYS454 3.2 41.1 1.0
C13 A:P1E701 3.4 22.2 1.0
CB A:ALA452 3.4 20.3 1.0
O A:HOH964 3.6 44.5 1.0
CG A:MET499 3.9 21.2 1.0
CG A:LYS454 4.0 26.4 1.0
CB A:MET499 4.1 18.7 1.0
NZ A:LYS454 4.2 44.3 1.0
CD A:LYS454 4.2 34.1 1.0
CG1 A:VAL436 4.3 24.7 1.0
N10 A:P1E701 4.3 21.6 1.0
O A:HOH807 4.3 41.1 1.0
N14 A:P1E701 4.5 21.8 1.0
C25 A:P1E701 4.6 24.4 1.0
CA A:ALA452 4.8 20.9 1.0
O A:HOH886 4.8 43.4 1.0
C9 A:P1E701 4.8 21.7 1.0
O A:ALA452 4.9 23.1 1.0
C A:ALA452 4.9 22.0 1.0

Fluorine binding site 2 out of 12 in 6yvy

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Fluorine binding site 2 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


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 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:28.9
occ:1.00
 F16 A:P1E701 0.0 28.9 1.0
C15 A:P1E701 1.3 26.3 1.0
F21 A:P1E701 2.1 26.6 1.0
F22 A:P1E701 2.1 27.2 1.0
C12 A:P1E701 2.3 23.2 1.0
N8 A:P1E701 3.0 22.3 1.0
C11 A:P1E701 3.0 22.2 1.0
O A:HOH886 3.1 43.4 1.0
O A:HOH807 3.3 41.1 1.0
O A:HOH964 3.3 44.5 1.0
C13 A:P1E701 3.4 22.2 1.0
CD1 A:LEU553 3.7 25.1 1.0
CE A:LYS454 3.9 41.1 1.0
NZ A:LYS454 4.1 44.3 1.0
O A:GLY563 4.1 33.5 1.0
N10 A:P1E701 4.3 21.6 1.0
C25 A:P1E701 4.4 24.4 1.0
C30 A:P1E701 4.4 27.9 1.0
N14 A:P1E701 4.6 21.8 1.0
O A:HOH977 4.6 31.6 1.0
CG A:MET499 4.8 21.2 1.0
C24 A:P1E701 4.8 26.2 1.0
CG A:LEU553 4.8 23.3 1.0
C9 A:P1E701 4.9 21.7 1.0

Fluorine binding site 3 out of 12 in 6yvy

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Fluorine binding site 3 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


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 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:26.6
occ:1.00
 F21 A:P1E701 0.0 26.6 1.0
C15 A:P1E701 1.3 26.3 1.0
F16 A:P1E701 2.1 28.9 1.0
F22 A:P1E701 2.1 27.2 1.0
C12 A:P1E701 2.4 23.2 1.0
C13 A:P1E701 2.7 22.2 1.0
CB A:MET499 3.2 18.7 1.0
CG A:MET499 3.4 21.2 1.0
C11 A:P1E701 3.7 22.2 1.0
O A:HOH807 3.7 41.1 1.0
CG2 A:VAL484 3.7 25.1 1.0
O A:GLU500 3.9 23.6 1.0
N14 A:P1E701 4.0 21.8 1.0
CB A:ALA452 4.1 20.3 1.0
CD1 A:LEU553 4.1 25.1 1.0
N8 A:P1E701 4.3 22.3 1.0
CE A:LYS454 4.4 41.1 1.0
CE A:MET499 4.5 18.8 1.0
CG1 A:VAL484 4.6 25.0 1.0
CB A:VAL484 4.7 24.4 1.0
CA A:MET499 4.7 18.9 1.0
N10 A:P1E701 4.7 21.6 1.0
C9 A:P1E701 4.8 21.7 1.0
SD A:MET499 4.8 26.1 1.0
O A:HOH886 4.9 43.4 1.0
O A:GLY563 5.0 33.5 1.0

Fluorine binding site 4 out of 12 in 6yvy

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Fluorine binding site 4 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:34.7
occ:1.00
 F22 B:P1E701 0.0 34.7 1.0
C15 B:P1E701 1.3 34.3 1.0
F21 B:P1E701 2.1 34.0 1.0
F16 B:P1E701 2.2 35.0 1.0
C12 B:P1E701 2.4 33.3 1.0
C11 B:P1E701 3.1 33.5 1.0
N8 B:P1E701 3.2 35.0 1.0
CE B:LYS454 3.3 52.6 1.0
C13 B:P1E701 3.4 32.7 1.0
CB B:ALA452 3.5 28.6 1.0
CG B:LYS454 4.1 41.2 1.0
CG B:MET499 4.2 33.0 1.0
CB B:MET499 4.2 29.4 1.0
NZ B:LYS454 4.2 55.1 1.0
CG1 B:VAL436 4.2 34.1 1.0
CD B:LYS454 4.3 47.0 1.0
N10 B:P1E701 4.3 32.8 1.0
C25 B:P1E701 4.5 37.4 1.0
N14 B:P1E701 4.6 32.3 1.0
C9 B:P1E701 4.8 32.9 1.0
CA B:ALA452 4.8 29.1 1.0
C28 B:P1E701 5.0 38.2 1.0

Fluorine binding site 5 out of 12 in 6yvy

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Fluorine binding site 5 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:35.0
occ:1.00
 F16 B:P1E701 0.0 35.0 1.0
C15 B:P1E701 1.3 34.3 1.0
F21 B:P1E701 2.1 34.0 1.0
F22 B:P1E701 2.2 34.7 1.0
C12 B:P1E701 2.4 33.3 1.0
N8 B:P1E701 3.0 35.0 1.0
C11 B:P1E701 3.1 33.5 1.0
C13 B:P1E701 3.5 32.7 1.0
CD1 B:LEU553 3.7 26.5 1.0
CE B:LYS454 3.9 52.6 1.0
NZ B:LYS454 4.1 55.1 1.0
N10 B:P1E701 4.3 32.8 1.0
C25 B:P1E701 4.4 37.4 1.0
C30 B:P1E701 4.5 40.0 1.0
N14 B:P1E701 4.6 32.3 1.0
O B:HOH919 4.8 33.6 1.0
C24 B:P1E701 4.8 38.8 1.0
C9 B:P1E701 4.9 32.9 1.0
O B:HOH891 4.9 47.4 1.0
CG B:LEU553 5.0 26.4 1.0

Fluorine binding site 6 out of 12 in 6yvy

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Fluorine binding site 6 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:34.0
occ:1.00
 F21 B:P1E701 0.0 34.0 1.0
C15 B:P1E701 1.3 34.3 1.0
F16 B:P1E701 2.1 35.0 1.0
F22 B:P1E701 2.1 34.7 1.0
C12 B:P1E701 2.4 33.3 1.0
C13 B:P1E701 2.7 32.7 1.0
CB B:MET499 3.4 29.4 1.0
CG1 B:VAL484 3.6 30.6 1.0
C11 B:P1E701 3.7 33.5 1.0
CG B:MET499 3.7 33.0 1.0
O B:GLU500 3.9 26.8 1.0
N14 B:P1E701 4.0 32.3 1.0
CB B:ALA452 4.1 28.6 1.0
CD1 B:LEU553 4.2 26.5 1.0
CE B:MET499 4.2 31.4 1.0
N8 B:P1E701 4.3 35.0 1.0
CE B:LYS454 4.4 52.6 1.0
CB B:VAL484 4.5 29.8 1.0
N10 B:P1E701 4.8 32.8 1.0
CA B:MET499 4.8 29.1 1.0
CG2 B:VAL484 4.8 30.4 1.0
C9 B:P1E701 4.8 32.9 1.0
SD B:MET499 4.9 37.7 1.0

Fluorine binding site 7 out of 12 in 6yvy

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Fluorine binding site 7 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:27.7
occ:1.00
 F22 C:P1E802 0.0 27.7 1.0
C15 C:P1E802 1.4 27.9 1.0
F21 C:P1E802 2.2 27.5 1.0
F16 C:P1E802 2.2 29.6 1.0
C12 C:P1E802 2.4 26.0 1.0
C11 C:P1E802 3.1 26.1 1.0
N8 C:P1E802 3.2 29.0 1.0
C13 C:P1E802 3.4 24.4 1.0
CB C:ALA452 3.8 20.0 1.0
CG C:MET499 3.9 21.4 1.0
CB C:MET499 3.9 19.0 1.0
CG C:LYS454 4.3 27.4 1.0
CD C:LYS454 4.3 31.7 1.0
N10 C:P1E802 4.3 23.8 1.0
CG1 C:VAL436 4.3 25.2 1.0
CB C:ASP564 4.5 36.2 1.0
C25 C:P1E802 4.5 31.3 1.0
N14 C:P1E802 4.6 23.6 1.0
C9 C:P1E802 4.9 23.1 1.0
CG C:ASP564 4.9 41.5 1.0
C28 C:P1E802 5.0 31.5 1.0

Fluorine binding site 8 out of 12 in 6yvy

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Fluorine binding site 8 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:29.6
occ:1.00
 F16 C:P1E802 0.0 29.6 1.0
C15 C:P1E802 1.3 27.9 1.0
F21 C:P1E802 2.1 27.5 1.0
F22 C:P1E802 2.2 27.7 1.0
C12 C:P1E802 2.3 26.0 1.0
N8 C:P1E802 3.1 29.0 1.0
C11 C:P1E802 3.1 26.1 1.0
CB C:ASP564 3.3 36.2 1.0
C13 C:P1E802 3.4 24.4 1.0
N C:ASP564 3.7 32.3 1.0
CD1 C:LEU553 3.7 22.0 1.0
CA C:ASP564 4.1 34.3 1.0
CG C:ASP564 4.3 41.5 1.0
N10 C:P1E802 4.3 23.8 1.0
CG2 C:VAL484 4.3 25.3 1.0
C30 C:P1E802 4.4 35.0 1.0
C25 C:P1E802 4.4 31.3 1.0
N14 C:P1E802 4.6 23.6 1.0
C C:GLY563 4.7 30.7 1.0
CA C:GLY563 4.8 27.6 1.0
C24 C:P1E802 4.8 33.0 1.0
OD2 C:ASP564 4.8 43.3 1.0
C9 C:P1E802 4.9 23.1 1.0
OD1 C:ASP564 4.9 41.7 1.0
CE C:MET499 4.9 22.3 1.0
CB C:VAL484 5.0 25.3 1.0

Fluorine binding site 9 out of 12 in 6yvy

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Fluorine binding site 9 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:27.5
occ:1.00
 F21 C:P1E802 0.0 27.5 1.0
C15 C:P1E802 1.4 27.9 1.0
F16 C:P1E802 2.1 29.6 1.0
F22 C:P1E802 2.2 27.7 1.0
C12 C:P1E802 2.4 26.0 1.0
C13 C:P1E802 2.7 24.4 1.0
CB C:MET499 3.2 19.0 1.0
O C:GLU500 3.5 19.8 1.0
CG C:MET499 3.7 21.4 1.0
C11 C:P1E802 3.7 26.1 1.0
CE C:MET499 3.8 22.3 1.0
CG2 C:VAL484 4.0 25.3 1.0
N14 C:P1E802 4.0 23.6 1.0
CB C:VAL484 4.2 25.3 1.0
CB C:ALA452 4.3 20.0 1.0
N8 C:P1E802 4.3 29.0 1.0
CG1 C:VAL484 4.4 27.3 1.0
CD1 C:LEU553 4.5 22.0 1.0
CB C:ASP564 4.5 36.2 1.0
CA C:MET499 4.6 19.2 1.0
SD C:MET499 4.7 25.4 1.0
C C:GLU500 4.7 20.4 1.0
N10 C:P1E802 4.8 23.8 1.0
C C:MET499 4.8 20.3 1.0
N C:GLU500 4.8 20.6 1.0
C9 C:P1E802 4.8 23.1 1.0

Fluorine binding site 10 out of 12 in 6yvy

Go back to Fluorine Binding Sites List in 6yvy
Fluorine binding site 10 out of 12 in the Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Focal Adhesion Kinase Catalytic Domain in Complex with 4-{[4-{[(1R, 2R)-2-(Dimethylamino)Cyclopentyl]Amino}-5-(Trifluoromethyl)Pyrimidin- 2-Yl]Amino}-N-Methylbenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F701

b:42.9
occ:1.00
 F22 D:P1E701 0.0 42.9 1.0
C15 D:P1E701 1.3 42.8 1.0
F21 D:P1E701 2.1 43.3 1.0
F16 D:P1E701 2.1 42.9 1.0
C12 D:P1E701 2.4 41.6 1.0
C11 D:P1E701 3.1 41.3 1.0
N8 D:P1E701 3.1 41.4 1.0
C13 D:P1E701 3.4 40.8 1.0
CB D:ALA452 3.5 34.5 1.0
CG D:MET499 3.9 45.5 1.0
CD D:LYS454 4.1 60.1 1.0
CB D:MET499 4.1 40.4 1.0
CG D:LYS454 4.1 54.7 1.0
NZ D:LYS454 4.2 67.5 1.0
CG1 D:VAL436 4.2 46.3 1.0
N10 D:P1E701 4.3 41.1 1.0
C25 D:P1E701 4.5 41.7 1.0
N14 D:P1E701 4.6 40.6 1.0
CE D:LYS454 4.8 64.8 1.0
C9 D:P1E701 4.8 41.2 1.0
CA D:ALA452 4.9 34.6 1.0
C28 D:P1E701 4.9 41.4 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: Tue Jul 15 17:58:17 2025

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