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Chlorine in PDB 3tt0: Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398)

Enzymatic activity of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398)

All present enzymatic activity of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398):
2.7.10.1;

Protein crystallography data

The structure of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398), PDB code: 3tt0 was solved by D.E.Bussiere, J.M.Murray, W.Shu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.86 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.110, 50.600, 66.900, 90.00, 107.27, 90.00
R / Rfree (%) 20.4 / 26.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398) (pdb code 3tt0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398), PDB code: 3tt0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3tt0

Go back to Chlorine Binding Sites List in 3tt0
Chlorine binding site 1 out of 4 in the Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:38.5
occ:1.00
 CL1 A:07J1 0.0 38.5 1.0
C5 A:07J1 1.7 46.9 1.0
C7 A:07J1 2.7 38.8 1.0
C4 A:07J1 2.7 39.3 1.0
O8 A:07J1 2.9 43.5 1.0
N3 A:07J1 3.0 42.9 1.0
CG1 A:VAL492 3.3 37.5 1.0
C2 A:07J1 3.4 39.6 1.0
O1 A:07J1 3.5 39.7 1.0
CG2 A:VAL492 3.6 43.0 1.0
CG2 A:VAL561 3.6 15.6 1.0
CB A:LYS514 3.7 31.8 1.0
C10 A:07J1 4.0 39.2 1.0
C14 A:07J1 4.0 39.7 1.0
CB A:VAL492 4.0 40.9 1.0
N A:LYS514 4.1 30.5 1.0
O A:HOH258 4.2 33.4 1.0
CB A:ALA512 4.2 45.4 1.0
CG A:LYS514 4.3 32.7 1.0
C9 A:07J1 4.3 38.5 1.0
C A:VAL513 4.3 29.8 1.0
CA A:LYS514 4.3 35.4 1.0
O A:ALA512 4.3 29.9 1.0
CD A:LYS514 4.3 40.7 1.0
C A:ALA512 4.4 34.2 1.0
N16 A:07J1 4.4 40.0 1.0
C11 A:07J1 4.5 39.6 1.0
O A:VAL513 4.6 30.1 1.0
N A:VAL513 4.6 28.0 1.0
N23 A:07J1 4.7 39.3 1.0
O A:VAL559 4.7 18.5 1.0
CA A:VAL513 4.9 28.8 1.0
CB A:VAL561 4.9 15.6 1.0
CA A:ALA512 5.0 26.6 1.0
CA A:VAL492 5.0 44.2 1.0

Chlorine binding site 2 out of 4 in 3tt0

Go back to Chlorine Binding Sites List in 3tt0
Chlorine binding site 2 out of 4 in the Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:40.2
occ:1.00
 CL2 A:07J1 0.0 40.2 1.0
C14 A:07J1 1.7 39.7 1.0
C4 A:07J1 2.7 39.3 1.0
C11 A:07J1 2.7 39.6 1.0
O12 A:07J1 2.9 40.0 1.0
N3 A:07J1 2.9 42.9 1.0
CB A:ALA640 3.2 17.9 1.0
C2 A:07J1 3.6 39.6 1.0
CG1 A:ILE545 3.6 21.0 1.0
CA A:ALA640 3.7 24.8 1.0
CD1 A:LEU630 3.7 30.2 1.0
CG2 A:ILE545 3.8 24.7 1.0
CB A:ILE545 3.8 20.5 1.0
N A:ASP641 3.9 28.2 1.0
C5 A:07J1 4.0 46.9 1.0
C10 A:07J1 4.0 39.2 1.0
O1 A:07J1 4.0 39.7 1.0
C13 A:07J1 4.3 39.9 1.0
C A:ALA640 4.3 26.0 1.0
OD2 A:ASP641 4.4 52.5 1.0
N23 A:07J1 4.4 39.3 1.0
N16 A:07J1 4.4 40.0 1.0
C7 A:07J1 4.5 38.8 1.0
CD1 A:ILE545 4.6 22.0 1.0
C18 A:07J1 4.7 40.1 1.0
O A:HOH258 4.8 33.4 1.0
CG A:ASP641 4.9 49.9 1.0
CA A:ASP641 5.0 31.4 1.0
N A:ALA640 5.0 17.6 1.0

Chlorine binding site 3 out of 4 in 3tt0

Go back to Chlorine Binding Sites List in 3tt0
Chlorine binding site 3 out of 4 in the Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1

b:36.3
occ:1.00
 CL1 B:07J1 0.0 36.3 1.0
C5 B:07J1 1.7 44.6 1.0
C7 B:07J1 2.7 44.6 1.0
C4 B:07J1 2.7 35.8 1.0
O8 B:07J1 2.9 40.3 1.0
N3 B:07J1 3.0 36.6 1.0
C2 B:07J1 3.4 42.6 1.0
O1 B:07J1 3.5 41.3 1.0
CG2 B:VAL561 3.5 20.2 1.0
CG1 B:VAL492 3.6 47.1 1.0
CG2 B:VAL492 3.6 49.0 1.0
CB B:LYS514 3.8 31.4 0.5
CB B:LYS514 3.8 30.9 0.5
C14 B:07J1 4.0 35.3 1.0
C10 B:07J1 4.0 40.5 1.0
O B:HOH110 4.2 29.9 1.0
CB B:ALA512 4.2 45.4 1.0
CD B:LYS514 4.2 32.4 0.5
CB B:VAL492 4.3 48.3 1.0
C9 B:07J1 4.3 34.0 1.0
N B:LYS514 4.4 35.7 1.0
N16 B:07J1 4.4 51.5 1.0
CG B:LYS514 4.4 31.8 0.5
O B:ALA512 4.4 31.7 1.0
C B:VAL513 4.5 25.7 1.0
C11 B:07J1 4.5 39.9 1.0
C B:ALA512 4.5 36.0 1.0
CA B:LYS514 4.5 32.6 0.5
CA B:LYS514 4.5 33.1 0.5
N23 B:07J1 4.6 37.7 1.0
CG B:LYS514 4.7 31.5 0.5
O B:VAL513 4.7 26.4 1.0
CD B:LYS514 4.8 32.1 0.5
N B:VAL513 4.8 25.7 1.0
CE B:LYS514 4.8 29.4 0.5
O B:VAL559 4.8 21.2 1.0
CB B:VAL561 4.8 18.9 1.0
CG1 B:VAL561 5.0 26.0 1.0
C18 B:07J1 5.0 51.5 1.0

Chlorine binding site 4 out of 4 in 3tt0

Go back to Chlorine Binding Sites List in 3tt0
Chlorine binding site 4 out of 4 in the Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Structure of Fibroblast Growth Factor Receptor 1 Kinase Domain with 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl-Piperazin-1- Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (BGJ398) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1

b:37.8
occ:1.00
 CL2 B:07J1 0.0 37.8 1.0
C14 B:07J1 1.7 35.3 1.0
C4 B:07J1 2.7 35.8 1.0
C11 B:07J1 2.7 39.9 1.0
N3 B:07J1 2.9 36.6 1.0
O12 B:07J1 2.9 39.9 1.0
CB B:ALA640 3.0 25.0 1.0
CA B:ALA640 3.6 25.6 1.0
C2 B:07J1 3.6 42.6 1.0
CD1 B:LEU630 3.6 30.6 1.0
N B:ASP641 3.7 28.4 1.0
CG1 B:ILE545 3.7 21.3 1.0
C5 B:07J1 4.0 44.6 1.0
C10 B:07J1 4.0 40.5 1.0
CG2 B:ILE545 4.0 25.3 1.0
CB B:ILE545 4.0 21.4 1.0
O1 B:07J1 4.1 41.3 1.0
OD2 B:ASP641 4.1 52.9 1.0
C B:ALA640 4.2 26.2 1.0
C13 B:07J1 4.3 41.9 1.0
N23 B:07J1 4.4 37.7 1.0
O B:HOH205 4.4 3.6 1.0
N16 B:07J1 4.4 51.5 1.0
C7 B:07J1 4.5 44.6 1.0
C18 B:07J1 4.6 51.5 1.0
O B:HOH110 4.6 29.9 1.0
CG B:ASP641 4.7 50.4 1.0
CD1 B:ILE545 4.7 21.0 1.0
CA B:ASP641 4.8 31.4 1.0
N B:ALA640 4.9 24.0 1.0
CG B:LEU630 4.9 27.9 1.0

Reference:

V.Guagnano, P.Furet, C.Spanka, V.Bordas, M.Le Douget, C.Stamm, J.Brueggen, M.R.Jensen, C.Schnell, H.Schmid, M.Wartmann, J.Berghausen, P.Drueckes, A.Zimmerlin, D.Bussiere, J.Murray, D.Graus Porta. Discovery of 3-(2,6-Dichloro-3,5-Dimethoxy-Phenyl)-1-{6-[4-(4-Ethyl- Piperazin-1-Yl)-Phenylamino]-Pyrimidin-4-Yl}-1-Methyl-Urea (Nvp-BGJ398), A Potent and Selective Inhibitor of the Fibroblast Growth Factor Receptor Family of Receptor Tyrosine Kinase. J.Med.Chem. V. 54 7066 2011.
ISSN: ISSN 0022-2623
PubMed: 21936542
DOI: 10.1021/JM2006222
Page generated: Fri Jul 11 10:55:10 2025

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