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Fluorine in PDB 4rg0: Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile

Enzymatic activity of Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile

All present enzymatic activity of Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile, PDB code: 4rg0 was solved by A.Kuglstatter, A.Wong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.76 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.937, 106.339, 38.429, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 28.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile (pdb code 4rg0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile, PDB code: 4rg0:

Fluorine binding site 1 out of 1 in 4rg0

Go back to Fluorine Binding Sites List in 4rg0
Fluorine binding site 1 out of 1 in the Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Btk Kinase Domain Complexed with 2-[8-Fluoro-2- [2-(Hydroxymethyl)-3-[1-Methyl-5-[[5-(4-Methylpiperazin-1-Yl)-2- Pyridyl]Amino]-6-Oxo-3-Pyridyl]Phenyl]-1-Oxo-3,4-Dihydroisoquinolin- 6-Yl]-2-Methyl-Propanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:32.3
occ:1.00
 F47 A:3P0701 0.0 32.3 1.0
C23 A:3P0701 1.4 31.5 1.0
C22 A:3P0701 2.3 30.9 1.0
C18 A:3P0701 2.4 31.6 1.0
O24 A:3P0701 2.7 28.2 1.0
O A:HOH1027 2.8 12.4 1.0
C17 A:3P0701 3.0 31.9 1.0
CD1 A:PHE413 3.2 32.6 1.0
C21 A:3P0701 3.6 31.0 1.0
C19 A:3P0701 3.7 32.4 1.0
NZ A:LYS430 3.7 27.2 1.0
N A:PHE413 3.8 31.1 1.0
N A:GLN412 3.9 31.1 1.0
CE1 A:PHE413 3.9 32.4 1.0
CD A:LYS430 4.0 29.3 1.0
CG A:PHE413 4.0 33.0 1.0
CE A:LYS430 4.1 27.8 1.0
OD2 A:ASP539 4.1 27.1 1.0
C20 A:3P0701 4.1 32.5 1.0
CB A:PHE413 4.2 33.3 1.0
N14 A:3P0701 4.3 32.1 1.0
CB A:GLN412 4.4 29.0 1.0
CA A:GLN412 4.5 30.6 1.0
C A:GLY411 4.5 30.9 1.0
C A:GLN412 4.6 31.3 1.0
CA A:GLY411 4.6 31.0 1.0
CA A:PHE413 4.6 32.6 1.0
CG A:ASP539 4.7 27.8 1.0
C41 A:3P0701 4.9 29.2 1.0
C43 A:3P0701 4.9 28.1 1.0
C16 A:3P0701 5.0 32.9 1.0

Reference:

Y.Lou, Z.K.Sweeney, A.Kuglstatter, D.Davis, D.M.Goldstein, X.Han, J.Hong, B.Kocer, R.K.Kondru, R.Litman, J.Mcintosh, K.Sarma, J.Suh, J.Taygerly, T.D.Owens. Finding the Perfect Spot For Fluorine: Improving Potency Up to 40-Fold During A Rational Fluorine Scan of A Bruton'S Tyrosine Kinase (Btk) Inhibitor Scaffold. Bioorg.Med.Chem.Lett. 2014.
ISSN: ESSN 1464-3405
PubMed: 25466710
DOI: 10.1016/J.BMCL.2014.11.030
Page generated: Thu Aug 1 05:33:55 2024

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