Chlorine in PDB 4c9w: Crystal Structure of NUDT1 (MTH1) with R-Crizotinib

All present enzymatic activity of Crystal Structure of NUDT1 (MTH1) with R-Crizotinib:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of NUDT1 (MTH1) with R-Crizotinib, PDB code: 4c9w was solved by J.M.Elkins, E.Salah, M.Vollmar, K.Huber, G.Superti-Furga, K.R.Abdul Azeez, J.Raynor, T.Krojer, F.Von Delft, C.Bountra, A.Edwards, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 1.65
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.200, 59.960, 66.870, 90.00, 90.00, 90.00
R / Rfree (%)	14.871 / 21.812

The structure of Crystal Structure of NUDT1 (MTH1) with R-Crizotinib also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of NUDT1 (MTH1) with R-Crizotinib (pdb code 4c9w). 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 NUDT1 (MTH1) with R-Crizotinib, PDB code: 4c9w:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of NUDT1 (MTH1) with R-Crizotinib


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 NUDT1 (MTH1) with R-Crizotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1157 b:52.6 occ:0.50 O A:HOH2140 2.7 26.6 1.0 O A:TYR148 3.4 11.2 1.0 CG2 A:THR149 3.5 15.6 1.0 O A:HOH2138 3.8 42.4 1.0 C A:TYR148 4.0 8.9 1.0 O A:HOH2139 4.0 21.8 1.0 CB A:ASP147 4.1 11.2 1.0 N A:TYR148 4.2 8.6 1.0 O A:HOH2144 4.4 31.1 1.0 O A:HOH2141 4.6 39.7 1.0 CA A:TYR148 4.6 8.7 1.0 N A:THR149 4.7 9.1 1.0 OD2 A:ASP147 4.8 16.9 1.0 C A:ASP147 4.8 9.5 1.0 CA A:ASP147 4.9 10.3 1.0 CG A:ASP147 4.9 13.5 1.0 CB A:THR149 4.9 11.8 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of NUDT1 (MTH1) with R-Crizotinib


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 NUDT1 (MTH1) with R-Crizotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1158 b:37.9 occ:1.00 CL A:VGH1158 0.0 37.9 1.0 C13 A:VGH1158 1.7 31.6 1.0 C1 A:VGH1158 2.5 29.4 1.0 C3 A:VGH1158 2.7 33.8 1.0 C17 A:VGH1158 2.7 27.9 1.0 C21 A:VGH1158 3.1 24.1 1.0 O A:PHE27 3.5 48.6 1.0 C4 A:VGH1158 3.9 24.7 1.0 C2 A:VGH1158 4.0 32.3 1.0 C18 A:VGH1158 4.0 32.5 1.0 C A:PHE27 4.2 46.8 1.0 CB A:PHE27 4.2 40.5 1.0 O27 A:VGH1158 4.3 23.7 1.0 CZ2 A:TRP117 4.4 24.9 1.0 C12 A:VGH1158 4.5 37.1 1.0 C15 A:VGH1158 4.6 22.9 1.0 C7 A:VGH1158 4.6 34.3 1.0 NE1 A:TRP117 4.6 19.6 1.0 CE2 A:TRP117 4.7 23.0 1.0 N A:GLY28 4.8 44.7 1.0 CA A:GLY28 4.8 40.9 1.0 CA A:PHE27 4.9 37.8 1.0 C14 A:VGH1158 5.0 22.8 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of NUDT1 (MTH1) with R-Crizotinib


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 NUDT1 (MTH1) with R-Crizotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1158 b:36.4 occ:1.00 CL2 A:VGH1158 0.0 36.4 1.0 C18 A:VGH1158 1.7 32.5 1.0 C12 A:VGH1158 2.6 37.1 1.0 C17 A:VGH1158 2.7 27.9 1.0 F A:VGH1158 2.8 41.1 1.0 O27 A:VGH1158 2.8 23.7 1.0 C21 A:VGH1158 2.9 24.1 1.0 C15 A:VGH1158 3.6 22.9 1.0 C2 A:VGH1158 3.9 32.3 1.0 CD2 A:LEU9 3.9 9.3 1.0 C13 A:VGH1158 4.0 31.6 1.0 CG1 A:VAL83 4.1 8.1 1.0 N22 A:VGH1158 4.2 17.6 1.0 C19 A:VGH1158 4.2 20.5 1.0 CD1 A:LEU9 4.2 10.0 1.0 CG2 A:VAL83 4.2 7.6 1.0 C4 A:VGH1158 4.4 24.7 1.0 CG A:LEU9 4.4 8.3 1.0 C1 A:VGH1158 4.4 29.4 1.0 C3 A:VGH1158 4.5 33.8 1.0 CB A:LEU9 4.5 8.2 1.0 CE A:MET81 4.5 22.9 1.0 CE2 A:PHE72 4.5 17.2 1.0 ND2 A:ASN33 4.5 14.4 0.5 CB A:VAL83 4.8 7.5 1.0 O A:HOH2031 4.8 14.0 0.5 CZ A:PHE72 5.0 15.9 1.0

K.V.M.Huber, E.Salah, B.Radic, M.Gridling, J.M.Elkins, A.Stukalov, A.Jemth, C.Gokturk, K.Sanjiv, K.Stromberg, T.Pham, U.W.Berglund, J.Colinge, K.L.Bennett, J.I.Loizou, T.Helleday, S.Knapp, G.Superti-Furga. Stereospecific Targeting of MTH1 By (S)-Crizotinib As An Anticancer Strategy. Nature V. 508 222 2014.
ISSN: ISSN 0028-0836
PubMed: 24695225
DOI: 10.1038/NATURE13194