Fluorine in PDB 5vo1: Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine)

Enzymatic activity of Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine)

All present enzymatic activity of Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine):
2.7.11.25;

Protein crystallography data

The structure of Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine), PDB code: 5vo1 was solved by S.F.Harris, J.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.17 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.284, 39.823, 61.702, 90.00, 105.30, 90.00
R / Rfree (%) 16.6 / 24.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine) (pdb code 5vo1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine), PDB code: 5vo1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5vo1

Go back to Fluorine Binding Sites List in 5vo1
Fluorine binding site 1 out of 3 in the Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:22.1
occ:1.00
 F17 A:9FS501 0.0 22.1 1.0
C16 A:9FS501 1.3 21.9 1.0
F18 A:9FS501 2.1 20.4 1.0
F19 A:9FS501 2.2 20.6 1.0
C11 A:9FS501 2.4 21.5 1.0
C10 A:9FS501 2.7 21.0 1.0
CG2 A:VAL139 3.3 25.2 1.0
NE2 A:GLN136 3.5 30.6 1.0
O A:HOH683 3.6 17.7 1.0
O A:HOH641 3.7 17.1 1.0
CD A:GLN136 3.7 41.5 1.0
C12 A:9FS501 3.7 21.6 1.0
OE1 A:GLN136 3.9 35.2 1.0
CB A:GLN136 3.9 32.2 1.0
C9 A:9FS501 4.1 21.6 1.0
CG1 A:VAL139 4.3 25.5 1.0
N15 A:9FS501 4.3 20.9 1.0
CG A:GLN136 4.4 41.8 1.0
CB A:VAL139 4.4 25.6 1.0
CB A:LYS152 4.7 27.8 1.0
CG A:LYS152 4.7 34.0 1.0
CD A:LYS152 4.7 42.6 1.0
CD1 A:LEU243 4.7 22.6 1.0
N8 A:9FS501 4.8 23.6 1.0
N13 A:9FS501 4.8 21.0 1.0
C14 A:9FS501 4.9 20.2 1.0
O A:HOH661 4.9 19.2 1.0
C7 A:9FS501 4.9 23.0 1.0

Fluorine binding site 2 out of 3 in 5vo1

Go back to Fluorine Binding Sites List in 5vo1
Fluorine binding site 2 out of 3 in the Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:20.4
occ:1.00
 F18 A:9FS501 0.0 20.4 1.0
C16 A:9FS501 1.3 21.9 1.0
F17 A:9FS501 2.1 22.1 1.0
F19 A:9FS501 2.2 20.6 1.0
C11 A:9FS501 2.3 21.5 1.0
N15 A:9FS501 3.0 20.9 1.0
NE2 A:GLN136 3.0 30.6 1.0
C12 A:9FS501 3.1 21.6 1.0
OE1 A:GLN136 3.2 35.2 1.0
CD A:GLN136 3.4 41.5 1.0
CD1 A:LEU243 3.4 22.6 1.0
C10 A:9FS501 3.4 21.0 1.0
SD A:MET190 3.6 30.2 1.0
CE A:MET190 4.0 27.1 1.0
N13 A:9FS501 4.3 21.0 1.0
OG A:SER253 4.4 21.3 1.0
CB A:SER253 4.5 20.0 1.0
C9 A:9FS501 4.6 21.6 1.0
CG A:GLN136 4.6 41.8 1.0
CG A:LEU243 4.6 22.5 1.0
O A:HOH668 4.7 22.2 1.0
CB A:GLN136 4.8 32.2 1.0
CD2 A:LEU243 4.8 23.8 1.0
C14 A:9FS501 4.9 20.2 1.0
CD A:LYS152 5.0 42.6 1.0

Fluorine binding site 3 out of 3 in 5vo1

Go back to Fluorine Binding Sites List in 5vo1
Fluorine binding site 3 out of 3 in the Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dlk in Complex with Compound 10 (5-(1-Isopropyl-5-(3-(Oxetan-3-Yl)-3- Azabicyclo[3.1.0]Hexan-6-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl) Pyridin-2-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:20.6
occ:1.00
 F19 A:9FS501 0.0 20.6 1.0
C16 A:9FS501 1.4 21.9 1.0
F18 A:9FS501 2.2 20.4 1.0
F17 A:9FS501 2.2 22.1 1.0
C11 A:9FS501 2.4 21.5 1.0
C12 A:9FS501 3.1 21.6 1.0
N15 A:9FS501 3.1 20.9 1.0
CE A:MET190 3.4 27.1 1.0
C10 A:9FS501 3.4 21.0 1.0
SD A:MET190 3.6 30.2 1.0
CB A:LYS152 3.7 27.8 1.0
CB A:ALA150 4.0 24.8 1.0
N13 A:9FS501 4.3 21.0 1.0
CG1 A:VAL139 4.3 25.5 1.0
CG A:LYS152 4.4 34.0 1.0
CG2 A:VAL139 4.4 25.2 1.0
CD A:LYS152 4.4 42.6 1.0
OE1 A:GLN136 4.5 35.2 1.0
C9 A:9FS501 4.6 21.6 1.0
CA A:LYS152 4.6 25.6 1.0
N A:LYS152 4.7 25.7 1.0
CB A:MET190 4.7 23.1 1.0
CD A:GLN136 4.9 41.5 1.0
CG A:MET190 4.9 26.5 1.0
NE2 A:GLN136 4.9 30.6 1.0
C14 A:9FS501 4.9 20.2 1.0

Reference:

S.Patel, W.J.Meilandt, R.I.Erickson, J.Chen, G.Deshmukh, A.A.Estrada, R.N.Fuji, P.Gibbons, A.Gustafson, S.F.Harris, J.Imperio, W.Liu, X.Liu, Y.Liu, J.P.Lyssikatos, C.Ma, J.Yin, J.W.Lewcock, M.Siu. Selective Inhibitors of Dual Leucine Zipper Kinase (Dlk, MAP3K12) with Activity in A Model of Alzheimer'S Disease. J. Med. Chem. V. 60 8083 2017.
ISSN: ISSN 1520-4804
PubMed: 28929759
DOI: 10.1021/ACS.JMEDCHEM.7B00843
Page generated: Sun Dec 13 12:40:48 2020

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