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Fluorine in PDB 5ceo: Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile

Enzymatic activity of Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile

All present enzymatic activity of Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile:
2.7.11.25;

Protein crystallography data

The structure of Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile, PDB code: 5ceo 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) 35.64 / 2.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.820, 39.040, 62.790, 90.00, 107.37, 90.00
R / Rfree (%) 18.7 / 24.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile (pdb code 5ceo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile, PDB code: 5ceo:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5ceo

Go back to Fluorine Binding Sites List in 5ceo
Fluorine binding site 1 out of 2 in the Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile


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 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:44.2
occ:1.00
 F21 A:50D501 0.0 44.2 1.0
C19 A:50D501 1.4 43.4 1.0
F22 A:50D501 2.2 48.1 1.0
C18 A:50D501 2.4 39.4 1.0
C20 A:50D501 2.4 39.2 1.0
C17 A:50D501 3.0 39.1 1.0
O A:GLY132 3.1 43.8 1.0
N16 A:50D501 3.1 40.0 1.0
C A:GLY132 3.2 46.3 1.0
CG2 A:VAL139 3.4 36.8 1.0
CB A:VAL139 3.5 37.2 1.0
N A:SER133 3.5 47.2 1.0
N A:GLY134 3.6 55.7 1.0
CA A:SER133 3.8 49.3 1.0
CA A:GLY132 3.9 42.3 1.0
C A:SER133 3.9 56.9 1.0
O A:GLY137 3.9 53.7 1.0
C14 A:50D501 4.3 40.2 1.0
N A:VAL139 4.3 37.3 1.0
N A:GLY132 4.4 42.7 1.0
CA A:GLY134 4.4 57.8 1.0
CA A:VAL139 4.4 35.4 1.0
CG1 A:VAL139 4.6 36.1 1.0
O A:SER133 4.7 56.6 1.0
N15 A:50D501 4.8 37.5 1.0
C A:VAL131 4.9 46.7 1.0

Fluorine binding site 2 out of 2 in 5ceo

Go back to Fluorine Binding Sites List in 5ceo
Fluorine binding site 2 out of 2 in the Dlk in Complex with Inhibitor 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile


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 2-((6-(3,3-Difluoropyrrolidin-1-Yl)-4- (1-(Oxetan-3-Yl)Piperidin-4-Yl)Pyridin-2-Yl)Amino)Isonicotinonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:48.1
occ:1.00
 F22 A:50D501 0.0 48.1 1.0
C19 A:50D501 1.4 43.4 1.0
F21 A:50D501 2.2 44.2 1.0
C20 A:50D501 2.4 39.2 1.0
C18 A:50D501 2.5 39.4 1.0
N A:GLY134 3.5 55.7 1.0
N16 A:50D501 3.6 40.0 1.0
NE2 A:GLN197 3.6 44.5 1.0
CA A:GLY134 3.6 57.8 1.0
C17 A:50D501 3.6 39.1 1.0
O A:HOH603 3.7 37.6 1.0
N A:ALA135 4.0 66.3 1.0
C A:GLY134 4.1 67.7 1.0
CG2 A:VAL139 4.1 36.8 1.0
CD A:GLN197 4.2 50.6 1.0
C A:SER133 4.4 56.9 1.0
O A:GLY137 4.5 53.7 1.0
C A:ALA135 4.7 73.1 1.0
N A:GLN136 4.7 67.8 1.0
OE1 A:GLN197 4.8 49.1 1.0
CG A:GLN197 4.8 33.6 1.0
CB A:VAL139 4.8 37.2 1.0
C14 A:50D501 4.8 40.2 1.0
O A:GLN136 4.9 66.0 1.0
O A:ALA135 4.9 74.7 1.0
CA A:SER133 4.9 49.3 1.0
O A:GLY134 5.0 69.0 1.0
C A:GLN136 5.0 66.6 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: Tue Jul 15 02:51:05 2025

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