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Fluorine in PDB 5wdy: Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

Enzymatic activity of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

All present enzymatic activity of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6):
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6), PDB code: 5wdy was solved by X.Xie, D.Kohls, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.84 / 2.46
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.334, 62.267, 70.268, 67.13, 77.42, 74.74
R / Rfree (%) 22.8 / 28.5

Other elements in 5wdy:

The structure of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) (pdb code 5wdy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6), PDB code: 5wdy:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5wdy

Go back to Fluorine Binding Sites List in 5wdy
Fluorine binding site 1 out of 2 in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:65.4
occ:1.00
 F1 A:A6S902 0.0 65.4 1.0
C3 A:A6S902 1.4 65.1 1.0
C4 A:A6S902 2.4 60.1 1.0
C2 A:A6S902 2.4 60.2 1.0
CB A:ALA269 3.2 52.7 1.0
CA A:ALA269 3.3 59.4 1.0
CZ A:PHE283 3.4 54.0 1.0
CZ A:PHE265 3.6 68.9 1.0
CD1 A:LEU272 3.6 53.9 1.0
CD1 A:LEU299 3.7 67.0 1.0
C6 A:A6S902 3.7 57.5 1.0
C1 A:A6S902 3.7 55.6 1.0
CE1 A:PHE265 3.8 67.7 1.0
N A:ALA269 3.9 65.7 1.0
CE1 A:PHE283 3.9 53.2 1.0
OG A:SER286 4.0 66.1 1.0
CE2 A:PHE265 4.1 64.5 1.0
C5 A:A6S902 4.2 55.4 1.0
CB A:SER286 4.3 62.0 1.0
CE2 A:PHE283 4.3 55.8 1.0
O A:PHE265 4.3 61.4 1.0
CD1 A:PHE265 4.5 70.3 1.0
C A:GLU268 4.5 61.1 1.0
C A:ALA269 4.6 57.1 1.0
CD2 A:PHE265 4.7 71.1 1.0
CG A:LEU272 4.7 51.1 1.0
O A:GLU268 4.7 55.0 1.0
CG A:PHE265 4.9 70.8 1.0
O A:ALA269 4.9 58.3 1.0
N1 A:A6S902 4.9 54.8 1.0
CG A:LEU299 5.0 68.3 1.0

Fluorine binding site 2 out of 2 in 5wdy

Go back to Fluorine Binding Sites List in 5wdy
Fluorine binding site 2 out of 2 in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:68.1
occ:1.00
 F1 B:A6S503 0.0 68.1 1.0
C3 B:A6S503 1.4 71.4 1.0
C2 B:A6S503 2.4 67.8 1.0
C4 B:A6S503 2.4 63.6 1.0
CZ B:PHE283 3.0 54.0 1.0
CB B:ALA269 3.1 69.8 1.0
CB B:SER286 3.3 58.5 1.0
CA B:ALA269 3.5 63.7 1.0
CE1 B:PHE283 3.6 53.0 1.0
OG B:SER286 3.6 61.0 1.0
C1 B:A6S503 3.7 63.7 1.0
C6 B:A6S503 3.7 61.2 1.0
CE2 B:PHE283 4.0 55.3 1.0
CZ B:PHE265 4.0 93.7 1.0
CE2 B:PHE265 4.1 93.7 1.0
C5 B:A6S503 4.2 60.2 1.0
CD1 B:LEU272 4.2 52.8 1.0
N B:ALA269 4.2 67.2 1.0
O B:PHE265 4.5 79.3 1.0
CE1 B:PHE265 4.6 92.8 1.0
CA B:SER286 4.7 56.4 1.0
CD2 B:PHE265 4.7 92.8 1.0
C B:ALA269 4.8 65.7 1.0
CD1 B:PHE283 4.8 49.5 1.0
N1 B:A6S503 5.0 61.1 1.0

Reference:

K.Yamada, J.Levell, T.Yoon, D.Kohls, D.Yowe, D.F.Rigel, H.Imase, J.Yuan, K.Yasoshima, K.Dipetrillo, L.Monovich, L.Xu, M.Zhu, M.Kato, M.Jain, N.Idamakanti, P.Taslimi, T.Kawanami, U.A.Argikar, V.Kunjathoor, X.Xie, Y.I.Yagi, Y.Iwaki, Z.Robinson, H.M.Park. Optimization of Allosteric with-No-Lysine (Wnk) Kinase Inhibitors and Efficacy in Rodent Hypertension Models. J. Med. Chem. V. 60 7099 2017.
ISSN: ISSN 1520-4804
PubMed: 28771350
DOI: 10.1021/ACS.JMEDCHEM.7B00708
Page generated: Thu Aug 1 16:32:41 2024

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