Fluorine in PDB 7gqu: Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide

The structure of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide, PDB code: 7gqu was solved by M.Classen, J.Benz, D.Brugger, O.Tagliente, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.14 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.255, 83.802, 119.624, 90, 90, 90
R / Rfree (%)	18 / 20.9

The structure of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide (pdb code 7gqu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide, PDB code: 7gqu:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide


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 Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:29.0 occ:0.50 F A:X1L1002 0.0 29.0 0.5 F A:X1L1002 0.8 27.2 0.5 C1 A:X1L1002 1.2 26.7 0.5 C1 A:X1L1002 1.3 27.2 0.5 C A:X1L1002 1.7 23.3 0.5 F1 A:X1L1002 2.1 36.1 0.5 F1 A:X1L1002 2.2 37.6 0.5 C A:X1L1002 2.3 23.4 0.5 C2 A:X1L1002 2.4 22.4 0.5 C2 A:X1L1002 2.5 22.4 0.5 N A:X1L1002 2.6 27.8 0.5 N A:X1L1002 2.9 29.4 0.5 CG A:MET845 3.3 31.6 1.0 CB A:HIS916 3.5 30.3 1.0 N2 A:X1L1002 3.5 21.4 0.5 N2 A:X1L1002 3.6 21.4 0.5 CD2 A:HIS916 3.6 34.3 1.0 CG A:HIS916 3.7 29.0 1.0 C3 A:X1L1002 3.9 28.8 0.5 CB A:MET845 4.1 27.2 1.0 C3 A:X1L1002 4.2 29.3 0.5 NZ A:LYS898 4.2 47.8 1.0 CD A:LYS898 4.4 27.9 1.0 CE A:MET845 4.5 34.5 1.0 C13 A:X1L1002 4.6 21.9 0.5 NE2 A:HIS916 4.6 30.5 1.0 C13 A:X1L1002 4.7 21.9 0.5 ND1 A:HIS916 4.7 32.6 1.0 C A:MET845 4.8 21.2 1.0 SD A:MET845 4.8 44.6 1.0 O A:MET845 4.8 22.2 1.0 C4 A:X1L1002 4.8 25.2 0.5 CE1 A:PHE917 4.9 28.4 1.0 CA A:HIS916 4.9 27.2 1.0 CE A:LYS898 4.9 35.4 1.0 SD A:MET895 5.0 47.0 1.0 CZ A:PHE917 5.0 23.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide


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 Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:27.2 occ:0.50 F A:X1L1002 0.0 27.2 0.5 F A:X1L1002 0.8 29.0 0.5 C1 A:X1L1002 1.4 26.7 0.5 C1 A:X1L1002 1.5 27.2 0.5 F1 A:X1L1002 1.9 36.1 0.5 F1 A:X1L1002 2.1 37.6 0.5 C2 A:X1L1002 2.3 22.4 0.5 N A:X1L1002 2.3 27.8 0.5 C A:X1L1002 2.3 23.3 0.5 C2 A:X1L1002 2.4 22.4 0.5 N A:X1L1002 2.6 29.4 0.5 C A:X1L1002 2.8 23.4 0.5 CG A:MET845 3.5 31.6 1.0 N2 A:X1L1002 3.5 21.4 0.5 CB A:HIS916 3.5 30.3 1.0 N2 A:X1L1002 3.6 21.4 0.5 NZ A:LYS898 3.6 47.8 1.0 C3 A:X1L1002 3.6 28.8 0.5 CG A:HIS916 3.7 29.0 1.0 CD2 A:HIS916 3.8 34.3 1.0 CD A:LYS898 3.8 27.9 1.0 C3 A:X1L1002 3.9 29.3 0.5 CB A:MET845 4.0 27.2 1.0 SD A:MET895 4.3 47.0 1.0 CE A:LYS898 4.3 35.4 1.0 C13 A:X1L1002 4.5 21.9 0.5 C13 A:X1L1002 4.6 21.9 0.5 C4 A:X1L1002 4.6 25.2 0.5 ND1 A:HIS916 4.6 32.6 1.0 NE2 A:HIS916 4.7 30.5 1.0 C A:MET845 4.8 21.2 1.0 C4 A:X1L1002 4.8 24.2 0.5 CE A:MET895 4.9 32.4 1.0 N A:GLU846 5.0 24.3 1.0 CA A:HIS916 5.0 27.2 1.0 CE A:MET845 5.0 34.5 1.0 O A:MET845 5.0 22.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:36.1 occ:0.50 F1 A:X1L1002 0.0 36.1 0.5 F1 A:X1L1002 0.6 37.6 0.5 C1 A:X1L1002 1.4 27.2 0.5 C1 A:X1L1002 1.5 26.7 0.5 F A:X1L1002 1.9 27.2 0.5 F A:X1L1002 2.1 29.0 0.5 C A:X1L1002 2.3 23.4 0.5 C2 A:X1L1002 2.4 22.4 0.5 C2 A:X1L1002 2.5 22.4 0.5 C A:X1L1002 2.7 23.3 0.5 N A:X1L1002 3.1 27.8 0.5 N2 A:X1L1002 3.1 21.4 0.5 N2 A:X1L1002 3.1 21.4 0.5 CG A:GLU846 3.4 36.2 1.0 N A:X1L1002 3.4 29.4 0.5 N A:GLU846 3.5 24.3 1.0 CA A:GLU846 3.6 25.1 1.0 C A:MET845 3.7 21.2 1.0 SD A:MET895 3.7 47.0 1.0 CG A:MET845 3.7 31.6 1.0 CB A:MET845 3.9 27.2 1.0 O A:MET845 3.9 22.2 1.0 CB A:GLU846 4.1 28.9 1.0 C13 A:X1L1002 4.2 21.9 0.5 C3 A:X1L1002 4.2 28.8 0.5 C13 A:X1L1002 4.3 21.9 0.5 CA A:MET845 4.4 25.8 1.0 C3 A:X1L1002 4.5 29.3 0.5 CD A:GLU846 4.7 31.3 1.0 NZ A:LYS898 4.7 47.8 1.0 OE2 A:GLU846 4.7 36.4 1.0 C4 A:X1L1002 4.8 25.2 0.5 C19 A:X1L1002 4.8 21.1 0.5 CE A:MET895 4.8 32.4 1.0 C19 A:X1L1002 4.9 21.1 0.5 CD A:LYS898 5.0 27.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:37.6 occ:0.50 F1 A:X1L1002 0.0 37.6 0.5 F1 A:X1L1002 0.6 36.1 0.5 C1 A:X1L1002 1.1 27.2 0.5 C1 A:X1L1002 1.4 26.7 0.5 C A:X1L1002 1.8 23.4 0.5 F A:X1L1002 2.1 27.2 0.5 F A:X1L1002 2.2 29.0 0.5 C2 A:X1L1002 2.2 22.4 0.5 C A:X1L1002 2.3 23.3 0.5 C2 A:X1L1002 2.4 22.4 0.5 N2 A:X1L1002 2.7 21.4 0.5 N2 A:X1L1002 2.8 21.4 0.5 N A:X1L1002 3.1 27.8 0.5 N A:X1L1002 3.4 29.4 0.5 CG A:GLU846 3.5 36.2 1.0 CA A:GLU846 3.6 25.1 1.0 N A:GLU846 3.6 24.3 1.0 C A:MET845 3.8 21.2 1.0 O A:MET845 3.9 22.2 1.0 C13 A:X1L1002 4.0 21.9 0.5 CG A:MET845 4.0 31.6 1.0 C13 A:X1L1002 4.0 21.9 0.5 CB A:GLU846 4.1 28.9 1.0 SD A:MET895 4.2 47.0 1.0 CB A:MET845 4.2 27.2 1.0 C3 A:X1L1002 4.3 28.8 0.5 C19 A:X1L1002 4.5 21.1 0.5 C19 A:X1L1002 4.5 21.1 0.5 C3 A:X1L1002 4.5 29.3 0.5 CB A:TYR849 4.6 21.4 1.0 C4 A:X1L1002 4.7 25.2 0.5 CA A:MET845 4.7 25.8 1.0 CD A:GLU846 4.7 31.3 1.0 OE2 A:GLU846 4.8 36.4 1.0 C4 A:X1L1002 4.9 24.2 0.5 CG A:TYR849 4.9 20.6 1.0 C A:GLU846 4.9 27.1 1.0 C14 A:X1L1002 4.9 21.9 0.5 O3 A:X1L1002 4.9 21.5 0.5 O3 A:X1L1002 5.0 21.9 0.5 C14 A:X1L1002 5.0 21.5 0.5

K.A.Baltgalvis, K.N.Lamb, K.T.Symons, C.C.Wu, M.A.Hoffman, A.N.Snead, X.Song, T.Glaza, S.Kikuchi, J.C.Green, D.C.Rogness, B.Lam, M.E.Rodriguez-Aguirre, D.R.Woody, C.L.Eissler, S.Rodiles, S.M.Negron, S.M.Bernard, E.Tran, J.Pollock, A.Tabatabaei, V.Contreras, H.N.Williams, M.K.Pastuszka, J.J.Sigler, P.Pettazzoni, M.G.Rudolph, M.Classen, D.Brugger, C.Claiborne, J.M.Plancher, I.Cuartas, J.Seoane, L.E.Burgess, R.T.Abraham, D.S.Weinstein, G.M.Simon, M.P.Patricelli, T.M.Kinsella. Chemoproteomic Discovery of A Covalent Allosteric Inhibitor of Wrn Helicase Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07318-Y