Fluorine in PDB 6dwd: SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket

The structure of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dwd was solved by K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl, O.T.Keppler, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.477, 142.233, 98.790, 90.00, 114.10, 90.00
R / Rfree (%)	17.6 / 20.2

The structure of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket also contains other interesting chemical elements:

Magnesium	(Mg)	10 atoms
Sodium	(Na)	23 atoms

The binding sites of Fluorine atom in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket (pdb code 6dwd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dwd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ D:F701 b:16.0 occ:1.00 F2' D:HDV701 0.0 16.0 1.0 C2' D:HDV701 1.4 14.6 1.0 C3' D:HDV701 2.3 13.8 1.0 C1' D:HDV701 2.3 13.9 1.0 N9 D:HDV701 2.7 15.8 1.0 C8 D:HDV701 2.8 18.7 1.0 C4' D:HDV701 2.9 15.1 1.0 O4' D:HDV701 3.0 13.4 1.0 C5' D:HDV701 3.0 18.3 1.0 CE2 D:TYR374 3.2 11.4 1.0 O D:HOH908 3.4 22.0 1.0 CD2 D:TYR374 3.4 11.0 1.0 O3' D:HDV701 3.5 11.7 1.0 C4 D:HDV701 3.7 16.5 1.0 CZ D:TYR374 3.7 11.2 1.0 O5' D:HDV701 3.7 22.6 1.0 N7 D:HDV701 3.9 18.2 1.0 CG D:TYR374 3.9 10.5 1.0 NE2 D:HIS370 3.9 16.5 1.0 CE1 D:TYR315 4.0 12.9 1.0 CZ D:TYR315 4.1 14.3 1.0 CE1 D:TYR374 4.2 11.5 1.0 CE1 D:HIS370 4.2 17.8 1.0 OH D:TYR374 4.3 11.8 1.0 CD1 D:TYR374 4.3 11.1 1.0 OH D:TYR315 4.3 14.1 1.0 C5 D:HDV701 4.3 16.4 1.0 CD1 D:TYR315 4.4 11.4 1.0 N3 D:HDV701 4.5 18.8 1.0 CE2 D:TYR315 4.6 13.8 1.0 OD2 D:ASP319 4.8 11.4 1.0 CB D:TYR374 4.8 11.6 1.0 CD2 D:HIS370 4.8 14.4 1.0 O D:HOH1058 4.9 48.2 1.0 CG D:TYR315 4.9 11.0 1.0 CD2 D:TYR315 5.0 12.4 1.0

Fluorine binding site 2 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ D:F703 b:15.7 occ:1.00 F2' D:HDV703 0.0 15.7 1.0 C2' D:HDV703 1.4 13.1 1.0 C1' D:HDV703 2.4 13.8 1.0 C3' D:HDV703 2.4 13.0 1.0 C8 D:HDV703 2.6 16.2 1.0 N9 D:HDV703 2.7 14.7 1.0 O5' D:HDV703 2.8 16.7 1.0 O4' D:HDV703 3.1 12.9 1.0 C4' D:HDV703 3.1 13.5 1.0 CG1 B:VAL156 3.2 13.4 1.0 NE2 B:HIS376 3.2 16.2 1.0 CD2 B:HIS376 3.3 16.7 1.0 C5' D:HDV703 3.5 14.7 1.0 CZ B:PHE157 3.5 13.6 1.0 CE1 B:PHE157 3.6 12.9 1.0 O3' D:HDV703 3.6 11.4 1.0 O2A D:HDV703 3.8 15.9 1.0 N7 D:HDV703 3.9 15.9 1.0 PA D:HDV703 3.9 16.9 1.0 C4 D:HDV703 4.0 15.1 1.0 CE2 B:PHE157 4.1 13.0 1.0 CE1 B:HIS376 4.1 16.9 1.0 CD1 B:PHE157 4.2 12.5 1.0 CG B:HIS376 4.2 15.8 1.0 O B:VAL156 4.3 13.1 1.0 CB B:VAL156 4.6 13.1 1.0 ND1 B:HIS376 4.6 15.7 1.0 C5 D:HDV703 4.6 15.2 1.0 CD2 B:PHE157 4.7 13.3 1.0 CG B:PHE157 4.7 13.4 1.0 C B:VAL156 4.8 13.0 1.0 O3A D:HDV703 4.9 15.5 1.0 O B:ARG372 4.9 19.2 1.0 N3 D:HDV703 5.0 17.8 1.0

Fluorine binding site 3 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ C:F701 b:21.1 occ:1.00 F2' C:HDV701 0.0 21.1 1.0 C2' C:HDV701 1.4 17.9 1.0 C3' C:HDV701 2.3 17.6 1.0 C1' C:HDV701 2.4 17.9 1.0 N9 C:HDV701 2.7 19.4 1.0 C8 C:HDV701 2.8 20.4 1.0 C4' C:HDV701 3.0 18.4 1.0 C5' C:HDV701 3.1 22.7 1.0 O4' C:HDV701 3.1 15.4 1.0 CE2 C:TYR374 3.2 15.4 1.0 O C:HOH902 3.2 26.9 1.0 CD2 C:TYR374 3.4 14.9 1.0 O3' C:HDV701 3.6 15.0 1.0 CZ C:TYR374 3.6 15.8 1.0 C4 C:HDV701 3.7 21.1 1.0 N7 C:HDV701 3.9 22.1 1.0 O5' C:HDV701 3.9 27.9 1.0 NE2 C:HIS370 3.9 19.0 1.0 CE1 C:TYR315 3.9 14.7 1.0 CG C:TYR374 4.0 13.8 1.0 CZ C:TYR315 4.1 14.1 1.0 CE1 C:TYR374 4.2 16.4 1.0 CE1 C:HIS370 4.2 20.9 1.0 OH C:TYR374 4.2 14.8 1.0 CD1 C:TYR374 4.3 15.3 1.0 OH C:TYR315 4.3 17.6 1.0 C5 C:HDV701 4.4 20.5 1.0 CD1 C:TYR315 4.4 13.5 1.0 N3 C:HDV701 4.5 22.6 1.0 CE2 C:TYR315 4.6 14.2 1.0 OD2 C:ASP319 4.7 12.7 1.0 CD2 C:HIS370 4.8 15.6 1.0 CB C:TYR374 4.8 14.9 1.0 CG C:TYR315 4.9 12.3 1.0

Fluorine binding site 4 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ C:F704 b:12.1 occ:1.00 F2' C:HDV704 0.0 12.1 1.0 C2' C:HDV704 1.4 10.5 1.0 C1' C:HDV704 2.3 10.9 1.0 C3' C:HDV704 2.4 10.3 1.0 C8 C:HDV704 2.6 12.8 1.0 N9 C:HDV704 2.7 12.4 1.0 O5' C:HDV704 2.8 11.6 1.0 O4' C:HDV704 3.0 10.2 1.0 C4' C:HDV704 3.1 10.0 1.0 CG1 A:VAL156 3.2 10.1 1.0 NE2 A:HIS376 3.3 11.4 1.0 CD2 A:HIS376 3.3 10.8 1.0 CZ A:PHE157 3.5 10.9 1.0 CE1 A:PHE157 3.6 10.6 1.0 C5' C:HDV704 3.6 10.1 1.0 O3' C:HDV704 3.6 9.9 1.0 O1A C:HDV704 3.7 9.9 1.0 PA C:HDV704 3.8 10.6 1.0 N7 C:HDV704 3.9 12.5 1.0 C4 C:HDV704 4.0 13.5 1.0 CE2 A:PHE157 4.2 11.9 1.0 CD1 A:PHE157 4.2 10.9 1.0 CE1 A:HIS376 4.2 11.0 1.0 CG A:HIS376 4.3 11.2 1.0 O A:VAL156 4.4 10.6 1.0 CB A:VAL156 4.6 10.1 1.0 C5 C:HDV704 4.6 12.0 1.0 CD2 A:PHE157 4.7 10.9 1.0 O2A C:HDV704 4.7 10.4 1.0 CG A:PHE157 4.7 10.6 1.0 ND1 A:HIS376 4.7 11.5 1.0 C A:VAL156 4.8 9.9 1.0 O A:ARG372 4.9 16.1 1.0 N3 C:HDV704 5.0 14.4 1.0 O3A C:HDV704 5.0 11.1 1.0

Fluorine binding site 5 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:13.5 occ:1.00 F2' B:HDV701 0.0 13.5 1.0 C2' B:HDV701 1.4 12.6 1.0 C3' B:HDV701 2.3 11.7 1.0 C1' B:HDV701 2.4 12.2 1.0 O5' B:HDV701 2.7 14.1 1.0 C8 B:HDV701 2.8 14.0 1.0 N9 B:HDV701 2.8 14.0 1.0 CG1 D:VAL156 3.0 11.5 1.0 C4' B:HDV701 3.1 11.7 1.0 O4' B:HDV701 3.2 12.5 1.0 NE2 D:HIS376 3.3 13.5 1.0 CD2 D:HIS376 3.4 13.1 1.0 C5' B:HDV701 3.5 14.3 1.0 O3' B:HDV701 3.5 10.8 1.0 CE1 D:PHE157 3.6 11.4 1.0 CZ D:PHE157 3.6 12.0 1.0 O1A B:HDV701 3.9 13.0 1.0 PA B:HDV701 4.0 13.6 1.0 N7 B:HDV701 4.1 15.1 1.0 CE1 D:HIS376 4.1 12.5 1.0 C4 B:HDV701 4.1 15.0 1.0 CD1 D:PHE157 4.1 10.9 1.0 CE2 D:PHE157 4.1 12.3 1.0 CG D:HIS376 4.2 12.7 1.0 O D:VAL156 4.3 11.5 1.0 CB D:VAL156 4.5 11.3 1.0 ND1 D:HIS376 4.6 12.2 1.0 CD2 D:PHE157 4.6 11.2 1.0 CG D:PHE157 4.6 10.4 1.0 C D:VAL156 4.7 10.3 1.0 C5 B:HDV701 4.8 15.0 1.0 O3A B:HDV701 4.9 15.4 1.0

Fluorine binding site 6 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F702 b:22.6 occ:1.00 F2' B:HDV702 0.0 22.6 1.0 C2' B:HDV702 1.4 20.9 1.0 C3' B:HDV702 2.3 18.9 1.0 C1' B:HDV702 2.4 21.1 1.0 N9 B:HDV702 2.7 24.0 1.0 C8 B:HDV702 2.8 26.4 1.0 C4' B:HDV702 2.9 19.4 1.0 C5' B:HDV702 3.0 22.9 1.0 O4' B:HDV702 3.1 18.5 1.0 CE2 B:TYR374 3.2 17.1 1.0 O B:HOH878 3.3 27.6 1.0 CD2 B:TYR374 3.4 15.7 1.0 O3' B:HDV702 3.6 15.5 1.0 CZ B:TYR374 3.6 15.4 1.0 C4 B:HDV702 3.7 23.9 1.0 O5' B:HDV702 3.8 33.0 1.0 N7 B:HDV702 3.9 23.8 1.0 CE1 B:TYR315 3.9 13.1 1.0 NE2 B:HIS370 4.0 19.7 1.0 CG B:TYR374 4.0 15.1 1.0 CZ B:TYR315 4.0 14.5 1.0 OH B:TYR374 4.2 14.6 1.0 CE1 B:TYR374 4.2 15.4 1.0 OH B:TYR315 4.3 16.4 1.0 CE1 B:HIS370 4.3 21.5 1.0 CD1 B:TYR374 4.3 16.7 1.0 C5 B:HDV702 4.3 22.6 1.0 CD1 B:TYR315 4.4 12.2 1.0 N3 B:HDV702 4.5 24.9 1.0 CE2 B:TYR315 4.6 14.3 1.0 OD2 B:ASP319 4.8 12.5 1.0 CD2 B:HIS370 4.9 17.7 1.0 CB B:TYR374 4.9 15.9 1.0 CG B:TYR315 4.9 12.6 1.0 CD2 B:TYR315 5.0 14.9 1.0

Fluorine binding site 7 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F702 b:14.8 occ:1.00 F2' A:HDV702 0.0 14.8 1.0 C2' A:HDV702 1.4 13.7 1.0 C1' A:HDV702 2.4 14.3 1.0 C3' A:HDV702 2.4 14.2 1.0 C8 A:HDV702 2.7 14.1 1.0 N9 A:HDV702 2.7 14.8 1.0 O5' A:HDV702 2.8 17.0 1.0 O4' A:HDV702 3.0 14.3 1.0 CG1 C:VAL156 3.1 17.2 1.0 NE2 C:HIS376 3.2 17.9 1.0 C4' A:HDV702 3.2 14.9 1.0 CD2 C:HIS376 3.3 18.7 1.0 CZ C:PHE157 3.6 13.3 1.0 C5' A:HDV702 3.6 15.6 1.0 CE1 C:PHE157 3.6 14.0 1.0 O3' A:HDV702 3.6 13.4 1.0 O2A A:HDV702 3.8 16.6 1.0 PA A:HDV702 4.0 16.4 1.0 N7 A:HDV702 4.0 14.1 1.0 C4 A:HDV702 4.0 16.3 1.0 CE1 C:HIS376 4.1 16.0 1.0 CE2 C:PHE157 4.1 13.8 1.0 CG C:HIS376 4.2 16.0 1.0 CD1 C:PHE157 4.2 14.0 1.0 O C:VAL156 4.4 14.1 1.0 CB C:VAL156 4.6 15.0 1.0 ND1 C:HIS376 4.6 15.8 1.0 C5 A:HDV702 4.6 15.7 1.0 CD2 C:PHE157 4.6 14.5 1.0 CG C:PHE157 4.7 13.7 1.0 C C:VAL156 4.8 13.4 1.0 O3A A:HDV702 4.9 18.7 1.0 O C:ARG372 4.9 17.0 1.0 O1A A:HDV702 5.0 18.7 1.0

Fluorine binding site 8 out of 8 in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:19.1 occ:1.00 F2' A:HDV704 0.0 19.1 1.0 C2' A:HDV704 1.5 14.8 1.0 C3' A:HDV704 2.3 14.6 1.0 C1' A:HDV704 2.5 15.2 1.0 N9 A:HDV704 2.8 17.3 1.0 C8 A:HDV704 2.9 19.3 1.0 C4' A:HDV704 3.0 15.8 1.0 C5' A:HDV704 3.0 19.0 1.0 O4' A:HDV704 3.1 13.2 1.0 CE2 A:TYR374 3.2 11.5 1.0 O A:HOH882 3.3 28.0 1.0 CD2 A:TYR374 3.4 11.5 1.0 O3' A:HDV704 3.6 11.5 1.0 CZ A:TYR374 3.6 10.4 1.0 O5' A:HDV704 3.8 25.9 1.0 C4 A:HDV704 3.8 18.8 1.0 CE1 A:TYR315 3.8 11.4 1.0 N7 A:HDV704 3.9 20.7 1.0 CZ A:TYR315 3.9 11.9 1.0 NE2 A:HIS370 4.0 15.4 1.0 CG A:TYR374 4.1 11.7 1.0 OH A:TYR315 4.1 13.4 1.0 OH A:TYR374 4.2 11.0 1.0 CE1 A:TYR374 4.2 10.5 1.0 CE1 A:HIS370 4.3 16.5 1.0 CD1 A:TYR315 4.3 11.0 1.0 CD1 A:TYR374 4.4 11.7 1.0 C5 A:HDV704 4.4 19.1 1.0 CE2 A:TYR315 4.5 11.2 1.0 N3 A:HDV704 4.6 20.4 1.0 OD2 A:ASP319 4.8 10.7 1.0 CD2 A:HIS370 4.8 16.5 1.0 CG A:TYR315 4.9 9.2 1.0 CD2 A:TYR315 4.9 10.3 1.0 CB A:TYR374 4.9 12.7 1.0

K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl Jr., O.T.Keppler, Y.Xiong. The Structural Basis For Cancer Drug Interactions with the Catalytic and Allosteric Sites of SAMHD1. Proc. Natl. Acad. Sci. V. 115 10022 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30305425
DOI: 10.1073/PNAS.1805593115