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Fluorine in PDB 7ejv: The Co-Crystal Structure of DYRK2 with Yk-2-69

Enzymatic activity of The Co-Crystal Structure of DYRK2 with Yk-2-69

All present enzymatic activity of The Co-Crystal Structure of DYRK2 with Yk-2-69:
2.7.12.1;

Protein crystallography data

The structure of The Co-Crystal Structure of DYRK2 with Yk-2-69, PDB code: 7ejv was solved by Z.Li, Y.Xiao, K.Yuan, W.Kuang, Y.Xiuquan, P.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.86, 129.387, 291.733, 90, 90, 90
R / Rfree (%) 20.1 / 24.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Co-Crystal Structure of DYRK2 with Yk-2-69 (pdb code 7ejv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the The Co-Crystal Structure of DYRK2 with Yk-2-69, PDB code: 7ejv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7ejv

Go back to Fluorine Binding Sites List in 7ejv
Fluorine binding site 1 out of 2 in the The Co-Crystal Structure of DYRK2 with Yk-2-69


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Co-Crystal Structure of DYRK2 with Yk-2-69 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:72.6
occ:1.00
F01 A:YK2501 0.0 72.6 1.0
C14 A:YK2501 1.4 76.0 1.0
C16 A:YK2501 2.3 77.7 1.0
C12 A:YK2501 2.4 67.8 1.0
C20 A:YK2501 2.8 67.8 1.0
C13 A:YK2501 3.0 67.0 1.0
CB A:PHE228 3.2 81.0 1.0
N07 A:YK2501 3.3 74.2 1.0
CG A:PHE228 3.6 79.2 1.0
CD1 A:ILE212 3.6 74.4 1.0
CB A:ALA176 3.7 71.5 1.0
N05 A:YK2501 3.7 64.0 1.0
CD1 A:PHE228 3.8 75.8 1.0
O A:GLU229 3.9 85.1 1.0
CG1 A:ILE212 4.0 74.5 1.0
C10 A:YK2501 4.0 71.0 1.0
C22 A:YK2501 4.1 68.9 1.0
C17 A:YK2501 4.3 64.9 1.0
CD2 A:PHE228 4.4 85.0 1.0
CA A:PHE228 4.5 90.1 1.0
CD1 A:LEU282 4.6 58.5 1.0
CG2 A:ILE294 4.6 71.7 1.0
CE1 A:PHE228 4.8 72.0 1.0
C A:PHE228 4.8 89.0 1.0
C A:GLU229 5.0 82.5 1.0

Fluorine binding site 2 out of 2 in 7ejv

Go back to Fluorine Binding Sites List in 7ejv
Fluorine binding site 2 out of 2 in the The Co-Crystal Structure of DYRK2 with Yk-2-69


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Co-Crystal Structure of DYRK2 with Yk-2-69 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:49.8
occ:1.00
F01 B:YK2501 0.0 49.8 1.0
C14 B:YK2501 1.4 51.0 1.0
C16 B:YK2501 2.3 50.0 1.0
C12 B:YK2501 2.5 42.0 1.0
C20 B:YK2501 2.8 42.8 1.0
C13 B:YK2501 3.0 47.1 1.0
CB B:PHE228 3.4 38.5 1.0
CG B:PHE228 3.5 39.9 1.0
N07 B:YK2501 3.6 41.7 1.0
CD1 B:ILE212 3.6 46.1 1.0
CD1 B:PHE228 3.7 38.0 1.0
CG1 B:ILE212 3.7 39.9 1.0
N05 B:YK2501 3.8 37.6 1.0
C10 B:YK2501 4.0 40.9 1.0
C22 B:YK2501 4.1 43.3 1.0
CG2 B:ILE294 4.2 44.0 1.0
CB B:ALA176 4.2 42.3 1.0
CD2 B:PHE228 4.3 38.9 1.0
O B:GLU229 4.3 47.6 1.0
C17 B:YK2501 4.4 45.1 1.0
CE1 B:PHE228 4.5 37.9 1.0
CD1 B:LEU282 4.6 49.6 1.0
CB B:ILE294 4.8 45.6 1.0
CB B:ILE212 4.8 41.9 1.0
CA B:PHE228 4.9 42.7 1.0

Reference:

K.Yuan, Z.Li, W.Kuang, X.Wang, M.Ji, W.Chen, J.Ding, J.Li, W.Min, C.Sun, X.Ye, M.Lu, L.Wang, H.Ge, Y.Jiang, H.Hao, Y.Xiao, P.Yang. Targeting Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase 2 with A Highly Selective Inhibitor For the Treatment of Prostate Cancer. Nat Commun V. 13 2903 2022.
ISSN: ESSN 2041-1723
PubMed: 35614066
DOI: 10.1038/S41467-022-30581-4
Page generated: Fri Aug 2 06:42:02 2024

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