Fluorine in PDB 8cie: Crystal Structure of the Human CDKL5 Kinase Domain with Compound Yl- 354

All present enzymatic activity of Crystal Structure of the Human CDKL5 Kinase Domain with Compound Yl- 354:
2.7.11.22;

The structure of Crystal Structure of the Human CDKL5 Kinase Domain with Compound Yl- 354, PDB code: 8cie was solved by W.Richardson, X.Chen, J.A.Newman, S.Bakshi, B.Lakshminarayana, L.Brooke, A.N.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.33 / 2.20
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	88.66, 88.66, 131.513, 90, 90, 120
R / Rfree (%)	28.8 / 31

The binding sites of Fluorine atom in the Crystal Structure of the Human CDKL5 Kinase Domain with Compound Yl- 354 (pdb code 8cie). 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 the Human CDKL5 Kinase Domain with Compound Yl- 354, PDB code: 8cie:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Human CDKL5 Kinase Domain with Compound Yl- 354


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 the Human CDKL5 Kinase Domain with Compound Yl- 354 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.5 occ:1.00 F1 A:US0401 0.0 33.5 1.0 C13 A:US0401 1.4 33.3 1.0 C14 A:US0401 2.3 33.1 1.0 C12 A:US0401 2.3 32.9 1.0 O A:HOH516 3.1 59.3 1.0 OE2 A:GLU139 3.3 43.5 1.0 OD1 A:ASN140 3.4 44.3 1.0 C15 A:US0401 3.6 33.3 1.0 C11 A:US0401 3.6 32.8 1.0 OH A:TYR24 3.6 45.8 1.0 CZ A:TYR24 3.8 48.9 1.0 CG A:GLU139 3.8 38.8 1.0 CD A:GLU139 3.9 41.1 1.0 CE2 A:TYR24 4.0 53.5 1.0 C16 A:US0401 4.1 33.0 1.0 CE1 A:TYR24 4.4 48.1 1.0 OD2 A:ASP153 4.6 49.1 1.0 CG A:ASN140 4.6 43.0 1.0 F2 A:US0401 4.7 34.1 1.0 CD2 A:TYR24 4.8 57.2 1.0 C1 A:US0401 4.8 32.3 1.0 CB A:ASP153 4.8 47.4 1.0 CG A:ASP153 4.9 50.1 1.0 O A:GLU139 4.9 35.2 1.0 SG A:CYS152 4.9 43.6 1.0 N1 A:US0401 4.9 31.5 1.0 OE1 A:GLU139 4.9 41.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Human CDKL5 Kinase Domain with Compound Yl- 354


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 the Human CDKL5 Kinase Domain with Compound Yl- 354 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:34.1 occ:1.00 F2 A:US0401 0.0 34.1 1.0 C15 A:US0401 1.4 33.3 1.0 C14 A:US0401 2.3 33.1 1.0 C16 A:US0401 2.3 33.0 1.0 OD1 A:ASP153 2.6 51.9 1.0 CG A:ASP153 3.0 50.1 1.0 CD1 A:TYR24 3.4 51.9 1.0 CD A:LYS42 3.4 64.9 1.0 C13 A:US0401 3.6 33.3 1.0 CE A:LYS42 3.6 68.2 1.0 C11 A:US0401 3.6 32.8 1.0 CG A:TYR24 3.6 56.5 1.0 OD2 A:ASP153 3.7 49.1 1.0 CB A:ASP153 3.7 47.4 1.0 CB A:TYR24 3.8 61.5 1.0 CA A:ASP153 3.9 50.0 1.0 CE1 A:TYR24 4.0 48.1 1.0 C12 A:US0401 4.1 32.9 1.0 NZ A:LYS42 4.2 69.2 1.0 CD2 A:TYR24 4.4 57.2 1.0 CG2 A:VAL27 4.5 38.2 1.0 F1 A:US0401 4.7 33.5 1.0 O A:TYR24 4.7 61.7 1.0 CZ A:TYR24 4.7 48.9 1.0 CG A:LYS42 4.7 63.6 1.0 N A:ASP153 4.8 48.4 1.0 C1 A:US0401 4.9 32.3 1.0 CE2 A:TYR24 4.9 53.5 1.0

H.W.Ong, Y.Liang, W.Richardson, E.R.Lowry, C.I.Wells, X.Chen, M.Silvestre, K.Dempster, J.A.Silvaroli, J.L.Smith, H.Wichterle, N.S.Pabla, S.K.Ultanir, A.N.Bullock, D.H.Drewry, A.D.Axtman. Discovery of A Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective Acs Chem Neurosci V. 14 1672 2023.
ISSN: ESSN 1948-7193
DOI: 10.1021/ACSCHEMNEURO.3C00135