Chlorine in PDB 4c9x: Crystal Structure of NUDT1 (MTH1) with S-Crizotinib

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

The structure of Crystal Structure of NUDT1 (MTH1) with S-Crizotinib, PDB code: 4c9x was solved by J.M.Elkins, E.Salah, M.Vollmar, K.Huber, G.Superti-Furga, K.R.Abdul Azeez, 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)	44.71 / 1.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.200, 60.020, 67.000, 90.00, 90.00, 90.00
R / Rfree (%)	14.629 / 18.159

The structure of Crystal Structure of NUDT1 (MTH1) with S-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 S-Crizotinib (pdb code 4c9x). 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 S-Crizotinib, PDB code: 4c9x:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of NUDT1 (MTH1) with S-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 S-Crizotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1157 b:26.6 occ:0.75 CL2 A:VHS1157 0.0 26.6 0.8 C18 A:VHS1157 1.7 20.3 0.8 C12 A:VHS1157 2.6 23.5 0.8 C17 A:VHS1157 2.7 16.5 0.8 F A:VHS1157 2.8 35.1 0.8 O27 A:VHS1157 2.9 13.3 0.8 C21 A:VHS1157 3.1 14.5 0.8 C1 A:VHS1157 3.4 16.4 0.8 C15 A:VHS1157 3.6 13.7 0.8 CE2 A:PHE72 3.8 9.0 0.2 O A:HOH2022 3.8 42.3 1.0 C2 A:VHS1157 3.9 23.5 0.8 CG1 A:VAL83 4.0 10.8 1.0 CD2 A:LEU9 4.0 12.2 1.0 C13 A:VHS1157 4.0 19.5 0.8 N22 A:VHS1157 4.1 11.7 0.8 C19 A:VHS1157 4.1 12.3 0.8 CG2 A:VAL83 4.2 10.2 1.0 CD1 A:LEU9 4.2 12.1 1.0 C4 A:VHS1157 4.3 14.6 0.8 CE2 A:PHE72 4.3 18.3 0.8 CZ A:PHE72 4.4 11.4 0.2 CG A:LEU9 4.5 10.2 1.0 CE A:MET81 4.5 16.6 0.2 C3 A:VHS1157 4.5 22.2 0.8 CB A:LEU9 4.5 8.4 1.0 CB A:VAL83 4.7 9.0 1.0 CD2 A:PHE72 4.7 8.6 0.2 O A:HOH2172 4.8 14.1 0.2 CZ A:PHE72 4.9 14.7 0.8

Chlorine binding site 2 out of 3 in the Crystal Structure of NUDT1 (MTH1) with S-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 S-Crizotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1157 b:24.6 occ:0.75 CL A:VHS1157 0.0 24.6 0.8 C13 A:VHS1157 1.7 19.5 0.8 C3 A:VHS1157 2.6 22.2 0.8 C17 A:VHS1157 2.7 16.5 0.8 C21 A:VHS1157 3.0 14.5 0.8 CE2 A:PHE27 3.5 34.2 1.0 CD2 A:PHE27 3.6 35.9 1.0 C2 A:VHS1157 3.9 23.5 0.8 C4 A:VHS1157 3.9 14.6 0.8 C1 A:VHS1157 3.9 16.4 0.8 C18 A:VHS1157 4.0 20.3 0.8 O27 A:VHS1157 4.2 13.3 0.8 CZ2 A:TRP117 4.3 23.4 1.0 O A:HOH2016 4.4 35.7 1.0 C12 A:VHS1157 4.4 23.5 0.8 C7 A:VHS1157 4.4 20.2 0.8 O A:HOH2054 4.5 35.6 1.0 C15 A:VHS1157 4.5 13.7 0.8 NE1 A:TRP117 4.5 19.1 1.0 CE2 A:TRP117 4.6 18.6 1.0 CZ A:PHE27 4.8 35.2 1.0 C14 A:VHS1157 4.9 16.0 0.8 C16 A:VHS1157 5.0 18.5 0.8 CG A:PHE27 5.0 36.0 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of NUDT1 (MTH1) with S-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 S-Crizotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1158 b:11.8 occ:0.75 O A:HOH2172 1.5 14.1 0.2 OD2 A:ASP120 3.0 12.8 1.0 O A:HOH2058 3.2 13.0 1.0 CB A:ASN33 3.3 16.4 1.0 N A:GLY34 3.4 9.1 1.0 N22 A:VHS1157 3.7 11.7 0.8 OD1 A:ASP120 3.7 10.5 1.0 CA A:ASN33 3.7 10.7 1.0 CG A:ASP120 3.7 9.5 1.0 CD2 A:LEU9 3.9 12.2 1.0 O27 A:VHS1157 4.1 13.3 0.8 C A:ASN33 4.1 8.2 1.0 CD1 A:LEU9 4.1 12.1 1.0 C1 A:VHS1157 4.2 16.4 0.8 CZ2 A:TRP123 4.3 8.8 1.0 CD1 A:TRP117 4.3 14.6 1.0 CA A:GLY34 4.4 9.1 1.0 CH2 A:TRP123 4.4 9.6 1.0 CG A:LEU9 4.6 10.2 1.0 CG A:ASN33 4.7 19.6 1.0 C19 A:VHS1157 4.7 12.3 0.8 C21 A:VHS1157 4.8 14.5 0.8 O A:TRP32 4.9 11.9 1.0 C15 A:VHS1157 4.9 13.7 0.8

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