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Fluorine in PDB 4agw: Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases

Enzymatic activity of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases

All present enzymatic activity of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases:
2.7.10.2;

Protein crystallography data

The structure of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases, PDB code: 4agw was solved by E.Weisberg, H.G.Choi, M.Seeliger, N.Gray, J.D.Griffin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.27 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.738, 61.393, 71.814, 79.57, 89.10, 90.14
R / Rfree (%) 22.6 / 27.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases (pdb code 4agw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases, PDB code: 4agw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4agw

Go back to Fluorine Binding Sites List in 4agw
Fluorine binding site 1 out of 6 in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1534

b:53.5
occ:1.00
 F1 A:NG71534 0.0 53.5 1.0
C A:NG71534 1.4 53.3 1.0
F2 A:NG71534 2.1 49.6 1.0
F3 A:NG71534 2.2 56.3 1.0
C22 A:NG71534 2.4 55.9 1.0
C21 A:NG71534 3.1 41.9 1.0
C24 A:NG71534 3.2 51.0 1.0
CG1 A:VAL402 3.3 40.1 1.0
C23 A:NG71534 3.4 51.2 1.0
CD2 A:HIS384 3.5 34.8 1.0
CB A:VAL402 3.9 41.3 1.0
O A:VAL402 4.0 48.8 1.0
NE2 A:HIS384 4.0 46.8 1.0
C A:VAL402 4.1 38.3 1.0
O A:ALA403 4.2 41.2 1.0
C20 A:NG71534 4.3 57.0 1.0
C A:ALA403 4.4 46.3 1.0
N05 A:NG71534 4.4 54.5 1.0
N A:ALA403 4.4 41.0 1.0
CD2 A:LEU322 4.5 35.7 1.0
CA A:ALA403 4.5 43.0 1.0
CG A:HIS384 4.5 42.7 1.0
CD1 A:LEU322 4.6 33.5 1.0
C18 A:NG71534 4.6 44.5 1.0
CG2 A:VAL377 4.7 43.9 1.0
CA A:VAL402 4.7 35.4 1.0
C28 A:NG71534 4.7 54.5 1.0
C19 A:NG71534 4.9 60.3 1.0
CB A:ASP404 4.9 54.2 1.0
N A:ASP404 5.0 50.1 1.0

Fluorine binding site 2 out of 6 in 4agw

Go back to Fluorine Binding Sites List in 4agw
Fluorine binding site 2 out of 6 in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1534

b:56.3
occ:1.00
 F3 A:NG71534 0.0 56.3 1.0
C A:NG71534 1.3 53.3 1.0
F2 A:NG71534 2.1 49.6 1.0
F1 A:NG71534 2.2 53.5 1.0
C22 A:NG71534 2.4 55.9 1.0
C24 A:NG71534 3.0 51.0 1.0
C21 A:NG71534 3.0 41.9 1.0
CD1 A:LEU322 3.1 33.5 1.0
CD1 A:LEU317 3.6 60.2 1.0
C23 A:NG71534 3.6 51.2 1.0
CG A:LEU322 4.1 40.6 1.0
CD2 A:LEU322 4.2 35.7 1.0
C20 A:NG71534 4.3 57.0 1.0
CG2 A:VAL377 4.3 43.9 1.0
N05 A:NG71534 4.4 54.5 1.0
CB A:LEU322 4.5 32.6 1.0
CB A:LEU317 4.5 54.9 1.0
CG A:LEU317 4.6 58.7 1.0
C18 A:NG71534 4.8 44.5 1.0
O A:VAL402 4.9 48.8 1.0

Fluorine binding site 3 out of 6 in 4agw

Go back to Fluorine Binding Sites List in 4agw
Fluorine binding site 3 out of 6 in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1534

b:49.6
occ:1.00
 F2 A:NG71534 0.0 49.6 1.0
C A:NG71534 1.3 53.3 1.0
F1 A:NG71534 2.1 53.5 1.0
F3 A:NG71534 2.1 56.3 1.0
C22 A:NG71534 2.5 55.9 1.0
C23 A:NG71534 2.8 51.2 1.0
O A:VAL402 3.0 48.8 1.0
C A:VAL402 3.7 38.3 1.0
C21 A:NG71534 3.7 41.9 1.0
CD1 A:LEU322 3.8 33.5 1.0
CB A:LEU322 3.9 32.6 1.0
N A:VAL323 4.0 49.3 1.0
CD2 A:LEU322 4.1 35.7 1.0
CA A:ALA403 4.1 43.0 1.0
CG A:LEU322 4.2 40.6 1.0
C18 A:NG71534 4.3 44.5 1.0
O A:VAL323 4.3 39.9 1.0
N A:ALA403 4.3 41.0 1.0
O A:NG71534 4.3 59.1 1.0
CB A:VAL402 4.3 41.3 1.0
CG1 A:VAL402 4.3 40.1 1.0
CA A:LEU322 4.4 33.7 1.0
C24 A:NG71534 4.4 51.0 1.0
C A:ALA403 4.6 46.3 1.0
C A:LEU322 4.6 43.0 1.0
CB A:VAL323 4.6 50.5 1.0
CA A:VAL402 4.7 35.4 1.0
C20 A:NG71534 4.8 57.0 1.0
CA A:VAL323 4.8 47.0 1.0
O A:ALA403 4.9 41.2 1.0
C A:VAL323 5.0 47.6 1.0

Fluorine binding site 4 out of 6 in 4agw

Go back to Fluorine Binding Sites List in 4agw
Fluorine binding site 4 out of 6 in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1534

b:56.0
occ:1.00
 F1 B:NG71534 0.0 56.0 1.0
C B:NG71534 1.3 50.1 1.0
F2 B:NG71534 2.1 50.9 1.0
F3 B:NG71534 2.1 58.8 1.0
C22 B:NG71534 2.4 56.5 1.0
C21 B:NG71534 3.0 48.1 1.0
CD2 B:HIS384 3.2 35.4 1.0
C24 B:NG71534 3.2 49.3 1.0
CG1 B:VAL402 3.4 38.9 1.0
C23 B:NG71534 3.5 51.2 1.0
NE2 B:HIS384 3.7 47.6 1.0
O B:ALA403 4.1 43.1 1.0
CB B:VAL402 4.2 40.7 1.0
CG B:HIS384 4.2 43.9 1.0
C B:ALA403 4.2 46.2 1.0
O B:VAL402 4.3 47.0 1.0
C20 B:NG71534 4.3 56.8 1.0
C B:VAL402 4.3 40.7 1.0
N05 B:NG71534 4.5 42.2 1.0
N B:ALA403 4.5 43.5 1.0
CA B:ALA403 4.5 46.0 1.0
CB B:ASP404 4.6 51.9 1.0
C18 B:NG71534 4.7 54.4 1.0
N B:ASP404 4.7 50.3 1.0
CE1 B:HIS384 4.8 45.9 1.0
CG B:LEU322 4.8 43.5 1.0
CB B:HIS384 4.9 42.1 1.0
CA B:VAL402 5.0 36.3 1.0
CG2 B:VAL377 5.0 42.4 1.0
C19 B:NG71534 5.0 58.1 1.0
C28 B:NG71534 5.0 45.4 1.0

Fluorine binding site 5 out of 6 in 4agw

Go back to Fluorine Binding Sites List in 4agw
Fluorine binding site 5 out of 6 in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1534

b:58.8
occ:1.00
 F3 B:NG71534 0.0 58.8 1.0
C B:NG71534 1.3 50.1 1.0
F2 B:NG71534 2.1 50.9 1.0
F1 B:NG71534 2.1 56.0 1.0
C22 B:NG71534 2.4 56.5 1.0
C21 B:NG71534 3.0 48.1 1.0
C24 B:NG71534 3.1 49.3 1.0
CD1 B:LEU317 3.5 42.1 1.0
C23 B:NG71534 3.5 51.2 1.0
CD2 B:LEU322 3.6 43.0 1.0
CG B:LEU322 3.8 43.5 1.0
C20 B:NG71534 4.3 56.8 1.0
CB B:LEU317 4.4 53.2 1.0
CG B:LEU317 4.6 57.5 1.0
N05 B:NG71534 4.6 42.2 1.0
CG2 B:VAL377 4.7 42.4 1.0
C18 B:NG71534 4.8 54.4 1.0
O B:VAL402 4.8 47.0 1.0
CB B:LEU322 4.8 41.3 1.0
CD1 B:LEU322 4.8 29.4 1.0
CG1 B:VAL402 5.0 38.9 1.0
C19 B:NG71534 5.0 58.1 1.0

Fluorine binding site 6 out of 6 in 4agw

Go back to Fluorine Binding Sites List in 4agw
Fluorine binding site 6 out of 6 in the Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Discovery of A Small Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1534

b:50.9
occ:1.00
 F2 B:NG71534 0.0 50.9 1.0
C B:NG71534 1.3 50.1 1.0
F3 B:NG71534 2.1 58.8 1.0
F1 B:NG71534 2.1 56.0 1.0
C22 B:NG71534 2.5 56.5 1.0
O B:VAL402 2.9 47.0 1.0
C23 B:NG71534 2.9 51.2 1.0
C B:VAL402 3.5 40.7 1.0
CA B:ALA403 3.7 46.0 1.0
C21 B:NG71534 3.8 48.1 1.0
CG B:LEU322 3.8 43.5 1.0
N B:ALA403 3.9 43.5 1.0
CG1 B:VAL402 4.0 38.9 1.0
C B:ALA403 4.0 46.2 1.0
CB B:VAL402 4.2 40.7 1.0
C18 B:NG71534 4.3 54.4 1.0
CD2 B:LEU322 4.4 43.0 1.0
CB B:LEU322 4.4 41.3 1.0
O B:ALA403 4.4 43.1 1.0
O B:NG71534 4.4 45.9 1.0
C24 B:NG71534 4.4 49.3 1.0
CA B:VAL402 4.5 36.3 1.0
N B:ASP404 4.5 50.3 1.0
N B:VAL323 4.5 47.3 1.0
O B:VAL323 4.6 37.8 1.0
CA B:LEU322 4.7 34.5 1.0
CB B:VAL323 4.7 46.7 1.0
CD1 B:LEU322 4.8 29.4 1.0
C20 B:NG71534 4.8 56.8 1.0
CD2 B:HIS384 5.0 35.4 1.0
C B:LEU322 5.0 44.5 1.0

Reference:

E.Weisberg, H.G.Choi, A.Ray, R.Barrett, J.Zhang, T.Sim, W.Zhou, M.Seeliger, M.Cameron, M.Azam, J.A.Fletcher, M.Debiec-Rychter, M.Mayeda, D.Moreno, A.L.Kung, P.A.Janne, R.Khosravi-Far, J.V.Melo, P.W.Manley, S.Adamia, C.Wu, N.Gray, J.D.Griffin. Discovery of A Small-Molecule Type II Inhibitor of Wild-Type and Gatekeeper Mutants of Bcr-Abl, Pdgfralpha, Kit, and Src Kinases: Novel Type II Inhibitor of Gatekeeper Mutants. Blood V. 115 4206 2010.
ISSN: ISSN 0006-4971
PubMed: 20299508
DOI: 10.1182/BLOOD-2009-11-251751
Page generated: Sun Dec 13 11:58:43 2020

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