Chlorine in PDB 5vcv: Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib

All present enzymatic activity of Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib:
2.7.11.1;

The structure of Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib, PDB code: 5vcv was solved by J.-Y.Zhu, M.P.Martin, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.56 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.130, 68.630, 75.440, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.7

The binding sites of Chlorine atom in the Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib (pdb code 5vcv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib, PDB code: 5vcv:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:19.2 occ:1.00 H A:ASP150 2.6 21.9 1.0 H A:LYS149 2.6 25.1 1.0 HA3 A:GLY147 2.7 24.3 1.0 HB3 A:LYS149 3.0 30.0 1.0 N A:LYS149 3.3 20.9 1.0 CA A:GLY147 3.3 20.3 1.0 C A:GLY147 3.4 19.4 1.0 HD2 A:PRO148 3.4 25.7 1.0 N A:ASP150 3.4 18.2 1.0 N A:PRO148 3.6 20.0 1.0 HB2 A:ASP150 3.7 22.5 1.0 CB A:LYS149 3.7 25.0 1.0 HB2 A:LYS149 3.8 30.0 1.0 O A:GLY147 3.8 18.4 1.0 CA A:LYS149 3.9 18.9 1.0 N A:GLY147 3.9 21.1 1.0 CD A:PRO148 3.9 21.4 1.0 HB3 A:ASP150 4.0 22.5 1.0 H A:GLY147 4.1 25.3 1.0 C A:LYS149 4.1 17.9 1.0 HA2 A:GLY147 4.2 24.3 1.0 CB A:ASP150 4.2 18.7 1.0 C A:PRO148 4.3 22.8 1.0 HD3 A:PRO148 4.4 25.7 1.0 CA A:ASP150 4.4 17.1 1.0 CA A:PRO148 4.5 19.4 1.0 C A:ARG146 4.5 20.3 1.0 O A:ARG146 4.7 21.5 1.0 HB2 A:ARG146 4.8 30.2 1.0 O A:HOH509 4.8 27.7 1.0 HA A:LYS149 4.8 22.7 1.0 HA A:ASP150 4.9 20.5 1.0 H A:ARG151 4.9 20.7 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:23.7 occ:1.00 HD2 A:PHE106 2.8 22.3 1.0 OH A:TYR184 2.9 17.5 1.0 HH21 A:ARG140 2.9 34.0 1.0 OG A:SER104 2.9 15.6 1.0 HB3 A:PHE106 3.0 16.9 1.0 HG A:SER104 3.1 18.7 1.0 HE2 A:TYR184 3.2 18.6 1.0 HG3 A:GLN107 3.3 32.6 1.0 HD2 A:ARG140 3.3 26.1 1.0 HH A:TYR184 3.4 20.9 1.0 HB3 A:SER104 3.6 19.5 1.0 NH2 A:ARG140 3.6 28.4 1.0 CD2 A:PHE106 3.7 18.6 1.0 HD3 A:ARG140 3.7 26.1 1.0 CB A:SER104 3.7 16.3 1.0 CZ A:TYR184 3.8 17.0 1.0 CE2 A:TYR184 3.9 15.5 1.0 HB2 A:SER104 3.9 19.5 1.0 CB A:PHE106 3.9 14.0 1.0 HH22 A:ARG140 3.9 34.0 1.0 CD A:ARG140 4.0 21.8 1.0 H A:GLN107 4.1 18.8 1.0 CG A:GLN107 4.2 27.2 1.0 HB2 A:PHE106 4.3 16.9 1.0 CG A:PHE106 4.3 13.9 1.0 HG2 A:GLN107 4.4 32.6 1.0 O A:HOH560 4.5 26.7 1.0 OE1 A:GLN107 4.6 23.1 1.0 CZ A:ARG140 4.6 32.6 1.0 N A:GLN107 4.7 15.6 1.0 HE2 A:PHE106 4.7 22.4 1.0 CE2 A:PHE106 4.7 18.6 1.0 H A:PHE106 4.7 20.7 1.0 CD A:GLN107 4.7 27.6 1.0 NE A:ARG140 4.8 24.2 1.0 O A:HOH563 4.8 13.1 1.0 HG3 A:ARG140 4.8 21.3 1.0 HH11 A:ARG112 4.9 69.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human MYT1 Kinase Domain in Complex with Dasatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:16.8 occ:1.00 CL A:1N1404 0.0 16.8 1.0 C5 A:1N1404 1.7 14.1 1.0 H A:ASP251 2.6 15.1 1.0 C6 A:1N1404 2.7 13.1 1.0 C4 A:1N1404 2.7 12.1 1.0 H6 A:1N1404 2.8 15.8 1.0 N2 A:1N1404 3.0 11.3 1.0 HA3 A:GLY250 3.0 14.5 1.0 HG21 A:VAL171 3.2 16.1 1.0 HG13 A:VAL171 3.3 19.1 1.0 C3 A:1N1404 3.4 12.0 1.0 HN2 A:1N1404 3.4 13.6 1.0 HE1 A:PHE240 3.4 15.4 1.0 N A:ASP251 3.4 12.6 1.0 O A:1N1404 3.5 11.6 1.0 HG12 A:VAL171 3.6 19.1 1.0 OD1 A:ASP251 3.6 32.9 1.0 HB A:VAL171 3.6 13.5 1.0 CG1 A:VAL171 3.8 15.9 1.0 CE1 A:PHE240 3.8 12.8 1.0 CA A:GLY250 3.8 12.1 1.0 O A:HOH516 3.9 29.4 1.0 HG21 A:THR187 3.9 12.9 1.0 HA2 A:GLY250 3.9 14.5 1.0 CG2 A:VAL171 4.0 13.4 1.0 C7 A:1N1404 4.0 12.2 1.0 CB A:VAL171 4.0 11.3 1.0 C9 A:1N1404 4.0 10.6 1.0 C A:GLY250 4.1 13.7 1.0 HA A:ASP251 4.1 15.3 1.0 HE1 A:HIS161 4.2 21.3 1.0 CZ A:PHE240 4.3 13.4 1.0 HZ A:PHE240 4.3 16.0 1.0 C2 A:1N1404 4.3 12.7 1.0 CA A:ASP251 4.4 12.7 1.0 CD1 A:PHE240 4.4 12.9 1.0 HG23 A:VAL171 4.5 16.1 1.0 HD1 A:PHE240 4.5 15.5 1.0 C8 A:1N1404 4.5 10.9 1.0 CG A:ASP251 4.6 76.2 1.0 HG22 A:VAL171 4.6 16.1 1.0 HG11 A:VAL171 4.7 19.1 1.0 H1 A:1N1404 4.7 15.5 1.0 H7 A:1N1404 4.8 14.6 1.0 CG2 A:THR187 4.9 10.8 1.0 C1 A:1N1404 4.9 12.9 1.0 CB A:ASP251 5.0 12.9 1.0

J.Y.Zhu, R.A.Cuellar, N.Berndt, H.E.Lee, S.H.Olesen, M.P.Martin, J.T.Jensen, G.I.Georg, E.Schonbrunn. Structural Basis of Wee Kinases Functionality and Inactivation By Diverse Small Molecule Inhibitors. J. Med. Chem. V. 60 7863 2017.
ISSN: ISSN 1520-4804
PubMed: 28792760
DOI: 10.1021/ACS.JMEDCHEM.7B00996