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

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

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

Protein crystallography data

The structure of Dlk in Complex with Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(Trifluoromethyl)Pyridin-2-Amine, PDB code: 5cep 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) 33.09 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.618, 39.617, 62.423, 90.00, 105.47, 90.00
R / Rfree (%) 17.2 / 23

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 3 in 5cep

Go back to Fluorine Binding Sites List in 5cep
Fluorine binding site 1 out of 3 in the Dlk in Complex with Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(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 Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(Trifluoromethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.1
occ:1.00
 F17 A:50E501 0.0 28.1 1.0
C16 A:50E501 1.3 29.7 1.0
F19 A:50E501 2.1 31.6 1.0
F18 A:50E501 2.2 32.2 1.0
C12 A:50E501 2.4 24.0 1.0
C13 A:50E501 2.9 22.9 1.0
NE2 A:GLN136 3.1 37.6 1.0
OE1 A:GLN136 3.1 39.5 1.0
CD A:GLN136 3.2 53.9 1.0
C11 A:50E501 3.5 24.6 1.0
CE A:MET190 3.7 28.6 1.0
CD1 A:LEU243 3.8 26.7 1.0
SD A:MET190 3.8 32.0 1.0
C14 A:50E501 4.2 24.8 1.0
CB A:GLN136 4.3 49.8 1.0
O A:HOH667 4.3 39.2 1.0
CG A:GLN136 4.4 55.5 1.0
OG A:SER253 4.5 23.0 1.0
C10 A:50E501 4.7 24.2 1.0
CB A:SER253 4.7 19.5 1.0
CE A:LYS152 4.9 57.1 1.0
CG A:LEU243 5.0 25.2 1.0
N15 A:50E501 5.0 22.6 1.0
O A:HOH736 5.0 45.4 1.0

Fluorine binding site 2 out of 3 in 5cep

Go back to Fluorine Binding Sites List in 5cep
Fluorine binding site 2 out of 3 in the Dlk in Complex with Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(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 Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(Trifluoromethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:32.2
occ:1.00
 F18 A:50E501 0.0 32.2 1.0
C16 A:50E501 1.3 29.7 1.0
F19 A:50E501 2.1 31.6 1.0
F17 A:50E501 2.2 28.1 1.0
C12 A:50E501 2.4 24.0 1.0
C13 A:50E501 3.1 22.9 1.0
C11 A:50E501 3.3 24.6 1.0
CE A:MET190 3.3 28.6 1.0
CG2 A:VAL139 3.4 32.5 1.0
CB A:LYS152 3.7 28.0 1.0
CG1 A:VAL139 3.9 31.9 1.0
CG A:LYS152 4.0 33.3 1.0
CB A:VAL139 4.3 32.9 1.0
C14 A:50E501 4.4 24.8 1.0
SD A:MET190 4.4 32.0 1.0
CA A:LYS152 4.4 25.6 1.0
CB A:ALA150 4.5 23.9 1.0
C10 A:50E501 4.5 24.2 1.0
NE2 A:GLN136 4.5 37.6 1.0
CD A:LYS152 4.8 42.1 1.0
O A:HOH736 4.8 45.4 1.0
N A:LYS152 4.8 24.7 1.0
CD A:GLN136 4.8 53.9 1.0
CB A:GLN136 4.9 49.8 1.0
OE1 A:GLN136 4.9 39.5 1.0
N15 A:50E501 5.0 22.6 1.0

Fluorine binding site 3 out of 3 in 5cep

Go back to Fluorine Binding Sites List in 5cep
Fluorine binding site 3 out of 3 in the Dlk in Complex with Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(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 Inhibitor N-(1-Isopropyl-5-(Piperidin-4-Yl)-1H- Pyrazol-3-Yl)-4-(Trifluoromethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:31.6
occ:1.00
 F19 A:50E501 0.0 31.6 1.0
C16 A:50E501 1.3 29.7 1.0
F18 A:50E501 2.1 32.2 1.0
F17 A:50E501 2.1 28.1 1.0
C12 A:50E501 2.4 24.0 1.0
C11 A:50E501 2.8 24.6 1.0
O A:HOH736 3.2 45.4 1.0
CG2 A:VAL139 3.3 32.5 1.0
C13 A:50E501 3.6 22.9 1.0
OE1 A:GLN136 3.7 39.5 1.0
CD A:GLN136 4.0 53.9 1.0
CB A:GLN136 4.0 49.8 1.0
C10 A:50E501 4.2 24.2 1.0
CG1 A:VAL139 4.3 31.9 1.0
NE2 A:GLN136 4.3 37.6 1.0
CB A:VAL139 4.4 32.9 1.0
N8 A:50E501 4.5 25.8 1.0
CG A:GLN136 4.6 55.5 1.0
CD1 A:LEU243 4.6 26.7 1.0
O A:HOH636 4.7 34.8 1.0
C14 A:50E501 4.7 24.8 1.0
CD2 A:LEU243 4.8 28.2 1.0
N15 A:50E501 5.0 22.6 1.0

Reference:

S.Patel, S.F.Harris, P.Gibbons, G.Deshmukh, A.Gustafson, T.Kellar, H.Lin, X.Liu, Y.Liu, Y.Liu, C.Ma, K.Scearce-Levie, A.S.Ghosh, Y.G.Shin, H.Solanoy, J.Wang, B.Wang, J.Yin, M.Siu, J.W.Lewcock. Scaffold-Hopping and Structure-Based Discovery of Potent, Selective, and Brain Penetrant N-(1H-Pyrazol-3-Yl)Pyridin-2-Amine Inhibitors of Dual Leucine Zipper Kinase (Dlk, MAP3K12). J.Med.Chem. V. 58 8182 2015.
ISSN: ISSN 0022-2623
PubMed: 26431428
DOI: 10.1021/ACS.JMEDCHEM.5B01072
Page generated: Thu Aug 1 08:30:13 2024

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