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Fluorine in PDB 4rfz: Crystal Structure of Btk Kinase Domain Complexed with 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One

Enzymatic activity of Crystal Structure of Btk Kinase Domain Complexed with 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One

All present enzymatic activity of Crystal Structure of Btk Kinase Domain Complexed with 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Btk Kinase Domain Complexed with 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One, PDB code: 4rfz 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) 42.72 / 1.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.936, 106.197, 38.220, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Btk Kinase Domain Complexed with 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One (pdb code 4rfz). 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 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One, PDB code: 4rfz:

Fluorine binding site 1 out of 1 in 4rfz

Go back to Fluorine Binding Sites List in 4rfz
Fluorine binding site 1 out of 1 in the Crystal Structure of Btk Kinase Domain Complexed with 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One


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 6- (Dimethylamino)-8-Fluoro-2-[2-(Hydroxymethyl)-3-[1-Methyl-5-[[5- (Morpholine-4-Carbonyl)-2-Pyridyl]Amino]-6-Oxo-3- Pyridyl]Phenyl]Isoquinolin-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:15.0
occ:1.00
 F46 A:3OV701 0.0 15.0 1.0
C40 A:3OV701 1.4 11.8 1.0
C39 A:3OV701 2.3 13.0 1.0
C35 A:3OV701 2.4 11.9 1.0
O44 A:3OV701 2.7 13.1 1.0
C34 A:3OV701 2.9 13.0 1.0
CD1 A:PHE413 3.2 13.7 1.0
NZ A:LYS430 3.2 12.4 1.0
CE A:LYS430 3.3 13.1 1.0
O A:HOH818 3.3 14.4 1.0
CD A:LYS430 3.6 13.4 1.0
C38 A:3OV701 3.6 11.5 1.0
C36 A:3OV701 3.6 12.9 1.0
OD2 A:ASP539 3.7 13.7 1.0
CE1 A:PHE413 3.7 14.4 1.0
C37 A:3OV701 4.1 13.3 1.0
CG A:PHE413 4.2 13.4 1.0
N31 A:3OV701 4.2 11.3 1.0
CG A:ASP539 4.3 12.6 1.0
N A:PHE413 4.4 13.7 1.0
CB A:PHE413 4.4 13.1 1.0
N A:GLN412 4.5 14.7 1.0
CD1 A:LEU542 4.6 13.7 1.0
CB A:GLN412 4.6 18.2 1.0
OD1 A:ASP539 4.6 14.3 1.0
OE1 A:GLN412 4.7 23.5 1.0
N41 A:3OV701 4.7 13.7 1.0
C33 A:3OV701 4.8 12.7 1.0
CG A:LYS430 4.9 11.5 1.0
O45 A:3OV701 4.9 11.4 1.0
CA A:GLN412 5.0 14.9 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: Tue Jul 15 00:37:57 2025

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