Fluorine in PDB 8v42: Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400

All present enzymatic activity of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400:
2.7.11.1;

The structure of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400, PDB code: 8v42 was solved by R.M.Counago, G.P.De Souza, A.Azevedo, C.Guimaraes, A.Mascarello, F.Gama, M.Ferreira, P.Arruda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.552, 96.615, 190.858, 90, 90, 90
R / Rfree (%)	19.9 / 23.1

The binding sites of Fluorine atom in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400 (pdb code 8v42). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400, PDB code: 8v42:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:71.5 occ:1.00 F1 B:YD9401 0.0 71.5 1.0 C11 B:YD9401 1.4 72.4 1.0 C12 B:YD9401 2.3 74.0 1.0 C10 B:YD9401 2.4 72.6 1.0 O1 B:YD9401 2.7 70.1 1.0 CB B:MET131 3.3 71.4 1.0 CE B:MET131 3.4 72.5 1.0 CG B:MET131 3.5 71.6 1.0 O B:HOH501 3.6 59.6 1.0 C9 B:YD9401 3.6 75.1 1.0 C7 B:YD9401 3.6 75.2 1.0 CB B:PRO111 3.6 57.4 1.0 CG B:PRO111 3.8 57.5 1.0 OH B:TYR87 4.1 56.2 1.0 C8 B:YD9401 4.1 75.6 1.0 SD B:MET131 4.3 74.9 1.0 CE2 B:PHE134 4.3 63.2 1.0 CG1 B:VAL196 4.4 53.9 1.0 CB B:VAL196 4.6 53.1 1.0 O B:ASP132 4.7 73.7 1.0 CA B:MET131 4.7 72.3 1.0 F2 B:YD9401 4.7 81.1 1.0 N5 B:YD9401 4.8 77.5 1.0 N B:ASP132 4.8 72.8 1.0 CZ B:TYR87 4.9 55.5 1.0 CE B:LYS71 4.9 84.5 1.0 NZ B:LYS71 5.0 82.4 1.0

Fluorine binding site 2 out of 4 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:81.1 occ:1.00 F2 B:YD9401 0.0 81.1 1.0 C9 B:YD9401 1.4 75.1 1.0 C8 B:YD9401 2.3 75.6 1.0 C10 B:YD9401 2.4 72.6 1.0 O1 B:YD9401 2.7 70.1 1.0 CE B:LYS71 3.2 84.5 1.0 NZ B:LYS71 3.2 82.4 1.0 C11 B:YD9401 3.6 72.4 1.0 C7 B:YD9401 3.6 75.2 1.0 C16 B:YD9401 3.8 94.6 1.0 CG2 B:VAL196 3.8 52.8 1.0 CD1 B:ILE51 4.1 99.7 1.0 CB B:VAL196 4.1 53.1 1.0 C15 B:YD9401 4.1 93.4 1.0 C12 B:YD9401 4.1 74.0 1.0 N B:ASP197 4.6 53.8 1.0 CD B:LYS71 4.6 85.4 1.0 F1 B:YD9401 4.7 71.5 1.0 CB B:ASP197 4.7 58.7 1.0 N5 B:YD9401 4.8 77.5 1.0 CG1 B:VAL196 4.8 53.9 1.0 N1 B:YD9401 4.8 82.0 1.0 CA B:ASP197 4.9 55.9 1.0 C14 B:YD9401 4.9 90.4 1.0

Fluorine binding site 3 out of 4 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400 within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:53.9 occ:1.00 F1 D:YD9503 0.0 53.9 1.0 C11 D:YD9503 1.4 57.6 1.0 C10 D:YD9503 2.4 58.6 1.0 C12 D:YD9503 2.4 59.9 1.0 O1 D:YD9503 2.7 56.3 1.0 O D:HOH601 3.2 58.4 1.0 CB D:MET131 3.3 64.5 1.0 CE D:MET131 3.4 61.7 1.0 CG D:MET131 3.5 63.0 1.0 C9 D:YD9503 3.6 61.3 1.0 C7 D:YD9503 3.6 62.4 1.0 CB D:PRO111 3.7 53.1 1.0 CG D:PRO111 3.9 52.9 1.0 C8 D:YD9503 4.1 62.7 1.0 OH D:TYR87 4.1 49.7 1.0 SD D:MET131 4.2 62.5 1.0 CE2 D:PHE134 4.3 58.6 1.0 CG1 D:VAL196 4.3 48.5 1.0 CB D:VAL196 4.4 47.5 1.0 O D:ASP132 4.6 70.2 1.0 CA D:MET131 4.7 67.0 1.0 F2 D:YD9503 4.7 62.6 1.0 N5 D:YD9503 4.8 66.7 1.0 CD D:LYS71 4.9 73.1 1.0 N D:ASP132 4.9 69.0 1.0

Fluorine binding site 4 out of 4 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH000400 within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:62.6 occ:1.00 F2 D:YD9503 0.0 62.6 1.0 C9 D:YD9503 1.4 61.3 1.0 C8 D:YD9503 2.3 62.7 1.0 C10 D:YD9503 2.4 58.6 1.0 O1 D:YD9503 2.7 56.3 1.0 NZ D:LYS71 3.5 72.7 1.0 C11 D:YD9503 3.6 57.6 1.0 C7 D:YD9503 3.6 62.4 1.0 C16 D:YD9503 3.6 82.2 1.0 CD1 D:ILE51 3.7 86.8 1.0 CE D:LYS71 3.8 73.4 1.0 CG2 D:VAL196 3.9 47.9 1.0 CD D:LYS71 4.1 73.1 1.0 C15 D:YD9503 4.1 80.9 1.0 C12 D:YD9503 4.1 59.9 1.0 CB D:VAL196 4.2 47.5 1.0 CB D:ASP197 4.6 51.1 1.0 N D:ASP197 4.7 46.6 1.0 F1 D:YD9503 4.7 53.9 1.0 N5 D:YD9503 4.8 66.7 1.0 N1 D:YD9503 4.8 70.2 1.0 CG D:LYS71 4.9 72.9 1.0 C14 D:YD9503 4.9 79.2 1.0 CA D:ASP197 4.9 48.5 1.0 CG1 D:VAL196 5.0 48.5 1.0

F.H.De Souza Gama, L.A.Dutra, M.Hawgood, C.V.Dos Reis, R.A.M.Serafim, M.A.Ferreira Jr., B.V.M.Teodoro, J.E.Takarada, A.S.Santiago, D.I.Balourdas, A.S.Nilsson, B.Urien, V.M.Almeida, C.Gileadi, P.Z.Ramos, A.Salmazo, S.N.S.Vasconcelos, M.R.Cunha, S.Mueller, S.Knapp, K.B.Massirer, J.M.Elkins, O.Gileadi, A.Mascarello, B.B.L.G.Lemmens, C.R.W.Guimaraes, H.Azevedo, R.M.Counago. Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1 Delta / Epsilon. J.Med.Chem. V. 67 8609 2024.
ISSN: ISSN 0022-2623
PubMed: 38780468
DOI: 10.1021/ACS.JMEDCHEM.3C02250