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Fluorine in PDB 4rfm: Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide

Enzymatic activity of Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide

All present enzymatic activity of Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide:
2.7.10.2;

Protein crystallography data

The structure of Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide, PDB code: 4rfm was solved by P.A.Mcewan, J.J.Barker, C.Eigenbrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.47 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.006, 69.561, 47.347, 90.00, 113.39, 90.00
R / Rfree (%) 20.3 / 26.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide (pdb code 4rfm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide, PDB code: 4rfm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4rfm

Go back to Fluorine Binding Sites List in 4rfm
Fluorine binding site 1 out of 2 in the Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:27.4
occ:1.00
 F35 A:3P6701 0.0 27.4 1.0
C34 A:3P6701 1.4 29.2 1.0
F36 A:3P6701 2.3 30.9 1.0
C2 A:3P6701 2.4 27.8 1.0
C33 A:3P6701 2.5 27.1 1.0
C3 A:3P6701 2.8 28.2 1.0
C32 A:3P6701 2.9 30.2 1.0
C4 A:3P6701 3.2 27.7 1.0
C31 A:3P6701 3.3 28.0 1.0
CG1 A:VAL377 3.4 27.7 1.0
CB A:ALA389 3.4 27.4 1.0
C1 A:3P6701 3.7 27.9 1.0
CD1 A:PHE435 3.7 29.1 1.0
CG2 A:VAL377 3.9 26.4 1.0
CB A:LYS391 4.0 31.5 1.0
C A:ALA389 4.2 29.4 1.0
N5 A:3P6701 4.3 27.9 1.0
CB A:PHE435 4.3 27.1 1.0
O A:ALA389 4.3 30.6 1.0
CB A:VAL377 4.3 25.9 1.0
CG A:PHE435 4.3 28.5 1.0
C7 A:3P6701 4.4 27.6 1.0
CA A:ALA389 4.4 29.4 1.0
CE1 A:PHE435 4.5 32.0 1.0
N A:ILE390 4.7 28.0 1.0
N A:LYS391 4.7 28.8 1.0
C A:ILE390 4.7 29.9 1.0
CG A:LYS391 4.7 36.4 1.0
CA A:LYS391 4.8 30.3 1.0
N6 A:3P6701 4.9 29.9 1.0
O A:ILE390 4.9 28.4 1.0

Fluorine binding site 2 out of 2 in 4rfm

Go back to Fluorine Binding Sites List in 4rfm
Fluorine binding site 2 out of 2 in the Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Itk Kinase Domain in Complex with Compound 1 N-{1-[(1,1-Dioxo-1-Thian- 2-Yl)(Phenyl)Methyl]-1H- Pyrazol-4-Yl}-5,5-Difluoro-5A-Methyl-1H,4H, 4AH,5H,5AH,6H-Cyclopropa[F]Indazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:30.9
occ:1.00
 F36 A:3P6701 0.0 30.9 1.0
C34 A:3P6701 1.4 29.2 1.0
F35 A:3P6701 2.3 27.4 1.0
C2 A:3P6701 2.5 27.8 1.0
C33 A:3P6701 2.5 27.1 1.0
C1 A:3P6701 2.8 27.9 1.0
CB A:LYS391 3.5 31.5 1.0
CG A:LYS391 3.6 36.4 1.0
CD1 A:PHE435 3.7 29.1 1.0
C32 A:3P6701 3.7 30.2 1.0
CE1 A:PHE435 3.7 32.0 1.0
C3 A:3P6701 3.7 28.2 1.0
CB A:PHE374 3.9 39.6 1.0
CG2 A:VAL377 4.1 26.4 1.0
CE A:LYS391 4.2 43.8 1.0
CG A:PHE374 4.4 43.2 1.0
CD1 A:PHE374 4.5 44.4 1.0
CD A:LYS391 4.5 40.4 1.0
C4 A:3P6701 4.6 27.7 1.0
O A:PHE374 4.6 35.2 1.0
CZ A:PHE435 4.6 30.2 1.0
C31 A:3P6701 4.6 28.0 1.0
CG A:PHE435 4.6 28.5 1.0
NZ A:LYS391 4.6 47.0 1.0
CA A:LYS391 4.9 30.3 1.0
CG1 A:VAL377 4.9 27.7 1.0

Reference:

J.D.Burch, K.Barrett, Y.Chen, J.Devoss, C.Eigenbrot, R.Goldsmith, M.H.Ismaili, K.Lau, Z.Lin, D.F.Ortwine, A.A.Zarrin, P.A.Mcewan, J.J.Barker, C.Ellebrandt, D.Kordt, D.B.Stein, X.Wang, Y.Chen, B.Hu, X.Xu, P.W.Yuen, Y.Zhang, Z.Pei. Tetrahydroindazoles As Interleukin-2 Inducible T-Cell Kinase Inhibitors. Part II. Second-Generation Analogues with Enhanced Potency, Selectivity, and Pharmacodynamic Modulation in Vivo. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25844760
DOI: 10.1021/JM501998M
Page generated: Tue Jul 15 00:37:52 2025

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