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Fluorine in PDB 5lj0: Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One

Enzymatic activity of Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One

All present enzymatic activity of Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One:
3.6.1.3;

Protein crystallography data

The structure of Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One, PDB code: 5lj0 was solved by C.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.55 / 1.82
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.158, 79.158, 135.857, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 18.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One (pdb code 5lj0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One, PDB code: 5lj0:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5lj0

Go back to Fluorine Binding Sites List in 5lj0
Fluorine binding site 1 out of 2 in the Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-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 Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1205

b:26.9
occ:1.00
 F31 A:6XX1205 0.0 26.9 1.0
C30 A:6XX1205 1.4 25.6 1.0
F32 A:6XX1205 2.2 26.7 1.0
C33 A:6XX1205 2.3 25.4 1.0
C27 A:6XX1205 2.3 25.7 1.0
NH1 A:ARG1077 3.1 22.6 1.0
O2 A:EDO1203 3.1 37.7 1.0
O A:HOH1320 3.5 40.1 1.0
O A:HOH1500 3.6 45.1 1.0
O A:HOH1536 3.6 49.8 1.0
O A:HOH1384 3.6 46.3 1.0
C24 A:6XX1205 3.7 25.3 1.0
C36 A:6XX1205 3.7 25.5 1.0
CB A:VAL1008 3.9 24.3 1.0
O A:HOH1368 4.0 22.9 1.0
C22 A:6XX1205 4.2 25.5 1.0
CG2 A:VAL1008 4.2 25.8 1.0
C2 A:EDO1203 4.4 42.2 1.0
CZ A:ARG1077 4.4 22.7 1.0
CG1 A:VAL1008 4.6 24.3 1.0
CA A:VAL1008 5.0 23.5 1.0

Fluorine binding site 2 out of 2 in 5lj0

Go back to Fluorine Binding Sites List in 5lj0
Fluorine binding site 2 out of 2 in the Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human ATAD2 Bromodomain in Complex with 8-(((3R, 4R,5S)-3-((4,4-Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl) Amino)-3-Methyl-5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1205

b:26.7
occ:1.00
 F32 A:6XX1205 0.0 26.7 1.0
C30 A:6XX1205 1.4 25.6 1.0
F31 A:6XX1205 2.2 26.9 1.0
C33 A:6XX1205 2.3 25.4 1.0
C27 A:6XX1205 2.3 25.7 1.0
C24 A:6XX1205 2.9 25.3 1.0
C36 A:6XX1205 2.9 25.5 1.0
NH1 A:ARG1077 3.3 22.6 1.0
C22 A:6XX1205 3.5 25.5 1.0
CB A:ILE1074 3.7 22.4 1.0
CG1 A:ILE1074 3.8 22.8 1.0
CB A:VAL1008 3.9 24.3 1.0
CG2 A:VAL1008 3.9 25.8 1.0
CD1 A:ILE1074 3.9 23.6 1.0
CG1 A:VAL1008 3.9 24.3 1.0
CA A:ILE1074 4.2 22.0 1.0
CD A:ARG1077 4.4 20.9 1.0
CZ A:ARG1077 4.5 22.7 1.0
O A:HOH1368 4.5 22.9 1.0
C19 A:6XX1205 4.6 25.7 1.0
N A:ILE1074 4.6 21.7 1.0
O2 A:EDO1203 4.7 37.7 1.0
NE A:ARG1077 4.9 21.7 1.0
CG2 A:ILE1074 4.9 22.9 1.0
CD2 A:LEU1073 5.0 22.7 1.0

Reference:

P.Bamborough, C.W.Chung, E.H.Demont, R.C.Furze, A.J.Bannister, K.H.Che, H.Diallo, C.Douault, P.Grandi, T.Kouzarides, A.M.Michon, D.J.Mitchell, R.K.Prinjha, C.Rau, S.Robson, R.J.Sheppard, R.Upton, R.J.Watson. A Chemical Probe For the ATAD2 Bromodomain. Angew.Chem.Int.Ed.Engl. V. 55 11382 2016.
ISSN: ESSN 1521-3773
PubMed: 27530368
DOI: 10.1002/ANIE.201603928
Page generated: Thu Aug 1 11:22:03 2024

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