Atomistry » Fluorine » PDB 4qte-4rv6 » 4rfm
Atomistry »
  Fluorine »
    PDB 4qte-4rv6 »
      4rfm »

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: Thu Aug 1 05:33:23 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy