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Fluorine in PDB 5vo2: Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7)

Enzymatic activity of Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7)

All present enzymatic activity of Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7):
2.7.11.25;

Protein crystallography data

The structure of Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7), PDB code: 5vo2 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) 35.79 / 2.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.290, 39.463, 60.113, 90.00, 104.81, 90.00
R / Rfree (%) 17 / 26.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7) (pdb code 5vo2). 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 Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7), PDB code: 5vo2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5vo2

Go back to Fluorine Binding Sites List in 5vo2
Fluorine binding site 1 out of 3 in the Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7)


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 Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.2
occ:1.00
 F17 A:9FV501 0.0 28.2 1.0
C16 A:9FV501 1.3 27.6 1.0
F19 A:9FV501 2.1 28.3 1.0
F18 A:9FV501 2.2 26.8 1.0
C11 A:9FV501 2.4 26.7 1.0
C10 A:9FV501 2.7 26.3 1.0
NE2 A:GLN136 3.5 44.1 1.0
CD A:GLN136 3.5 56.2 1.0
O A:HOH632 3.5 32.4 1.0
OE1 A:GLN136 3.6 53.0 1.0
CG2 A:VAL139 3.6 27.2 1.0
C12 A:9FV501 3.7 25.7 1.0
CB A:GLN136 3.8 35.3 1.0
C9 A:9FV501 4.1 26.2 1.0
CG A:GLN136 4.3 43.8 1.0
N15 A:9FV501 4.3 27.1 1.0
CD1 A:LEU243 4.4 23.6 1.0
CG1 A:VAL139 4.6 26.9 1.0
CE A:MET190 4.7 35.0 1.0
O A:HOH602 4.8 31.1 1.0
CB A:LYS152 4.8 25.4 1.0
CD2 A:LEU243 4.8 25.4 1.0
N8 A:9FV501 4.8 28.4 1.0
CB A:VAL139 4.8 27.4 1.0
N13 A:9FV501 4.8 24.6 1.0
C14 A:9FV501 4.9 24.0 1.0
C7 A:9FV501 5.0 28.4 1.0

Fluorine binding site 2 out of 3 in 5vo2

Go back to Fluorine Binding Sites List in 5vo2
Fluorine binding site 2 out of 3 in the Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7)


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 Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:26.8
occ:1.00
 F18 A:9FV501 0.0 26.8 1.0
C16 A:9FV501 1.3 27.6 1.0
F19 A:9FV501 2.1 28.3 1.0
F17 A:9FV501 2.2 28.2 1.0
C11 A:9FV501 2.4 26.7 1.0
N15 A:9FV501 2.9 27.1 1.0
C12 A:9FV501 3.0 25.7 1.0
OE1 A:GLN136 3.2 53.0 1.0
SD A:MET190 3.3 38.1 1.0
CE A:MET190 3.4 35.0 1.0
CD1 A:LEU243 3.5 23.6 1.0
C10 A:9FV501 3.6 26.3 1.0
NE2 A:GLN136 3.6 44.1 1.0
CD A:GLN136 3.7 56.2 1.0
N13 A:9FV501 4.3 24.6 1.0
O A:HOH601 4.7 19.5 1.0
CB A:MET190 4.7 30.5 1.0
CB A:SER253 4.7 21.1 1.0
OG A:SER253 4.7 23.0 1.0
CG A:MET190 4.7 34.0 1.0
C9 A:9FV501 4.8 26.2 1.0
CG A:LEU243 4.8 23.4 1.0
CD1 A:ILE174 4.9 26.1 1.0
CG A:GLN136 4.9 43.8 1.0
CG1 A:ILE174 5.0 21.8 1.0

Fluorine binding site 3 out of 3 in 5vo2

Go back to Fluorine Binding Sites List in 5vo2
Fluorine binding site 3 out of 3 in the Dlk in Complex with Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7)


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 Inhibitor 5-(1-Isopropyl-5-(1-(Oxetan-3-Yl) Piperidin-4-Yl)-1H-Pyrazol-3-Yl)-3-(Trifluoromethyl)Pyridin-2-Amine (Compound 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.3
occ:1.00
 F19 A:9FV501 0.0 28.3 1.0
C16 A:9FV501 1.3 27.6 1.0
F17 A:9FV501 2.1 28.2 1.0
F18 A:9FV501 2.1 26.8 1.0
C11 A:9FV501 2.4 26.7 1.0
C10 A:9FV501 3.2 26.3 1.0
CE A:MET190 3.2 35.0 1.0
C12 A:9FV501 3.3 25.7 1.0
N15 A:9FV501 3.5 27.1 1.0
CB A:LYS152 3.6 25.4 1.0
CB A:ALA150 4.0 26.4 1.0
CG2 A:VAL139 4.0 27.2 1.0
CG1 A:VAL139 4.1 26.9 1.0
SD A:MET190 4.1 38.1 1.0
OE1 A:GLN136 4.2 53.0 1.0
C9 A:9FV501 4.4 26.2 1.0
CA A:LYS152 4.5 23.8 1.0
N13 A:9FV501 4.5 24.6 1.0
CG A:LYS152 4.5 31.9 1.0
N A:LYS152 4.5 24.0 1.0
CD A:GLN136 4.7 56.2 1.0
CB A:VAL139 4.7 27.4 1.0
CD A:LYS152 4.8 39.4 1.0
C14 A:9FV501 4.9 24.0 1.0
C A:ALA150 4.9 27.8 1.0
NE2 A:GLN136 5.0 44.1 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: Thu Aug 1 16:09:44 2024

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