Fluorine in PDB 6tti: PKM2 in Complex with Compound 6

All present enzymatic activity of PKM2 in Complex with Compound 6:
2.7.1.40;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the PKM2 in Complex with Compound 6 (pdb code 6tti). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the PKM2 in Complex with Compound 6, PDB code: 6tti:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:50.0 occ:1.00 F11 A:NXE1001 0.0 50.0 1.0 C10 A:NXE1001 1.3 58.9 1.0 F12 A:NXE1001 2.1 47.5 1.0 F13 A:NXE1001 2.1 64.1 1.0 C7 A:NXE1001 2.4 61.5 1.0 C6 A:NXE1001 2.9 49.1 1.0 O A:ALA388 3.2 5.7 1.0 C1 A:DMS1003 3.4 36.3 1.0 NE2 A:HIS29 3.5 3.8 1.0 N8 A:NXE1001 3.6 53.1 1.0 CE1 A:PHE26 3.7 36.8 1.0 CD2 A:HIS29 3.7 3.6 1.0 CZ A:PHE26 4.0 49.8 1.0 C5 A:NXE1001 4.2 49.0 1.0 C A:ALA388 4.4 6.8 1.0 N A:TYR390 4.5 3.9 1.0 O9 A:NXE1001 4.6 48.3 1.0 CD2 A:LEU353 4.6 9.6 1.0 CB A:TYR390 4.6 0.8 1.0 CE1 A:HIS29 4.8 3.7 1.0 CD1 A:PHE26 4.8 34.5 1.0 CA A:ILE389 4.9 5.2 1.0 C A:ILE389 4.9 4.4 1.0 S A:DMS1003 5.0 35.2 1.0 CD1 A:LEU353 5.0 11.0 1.0

Fluorine binding site 2 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:47.5 occ:1.00 F12 A:NXE1001 0.0 47.5 1.0 C10 A:NXE1001 1.3 58.9 1.0 F13 A:NXE1001 2.1 64.1 1.0 F11 A:NXE1001 2.1 50.0 1.0 C7 A:NXE1001 2.4 61.5 1.0 N8 A:NXE1001 3.0 53.1 1.0 C6 A:NXE1001 3.5 49.1 1.0 O A:ALA388 3.7 5.7 1.0 CD1 A:LEU353 3.8 11.0 1.0 CD B:LYS311 4.0 19.4 1.0 CD2 A:LEU353 4.1 9.6 1.0 CD1 A:LEU33 4.2 15.0 1.0 CB A:ALA388 4.3 8.2 1.0 O9 A:NXE1001 4.3 48.3 1.0 C5 A:NXE1001 4.5 49.0 1.0 C A:ALA388 4.6 6.8 1.0 CG A:LEU353 4.6 9.5 1.0 NE2 A:HIS29 4.6 3.8 1.0 CE B:LYS311 4.8 30.8 1.0 CD2 A:HIS29 4.9 3.6 1.0 CD2 A:LEU33 5.0 15.0 1.0 CG B:LYS311 5.0 15.3 1.0

Fluorine binding site 3 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:64.1 occ:1.00 F13 A:NXE1001 0.0 64.1 1.0 C10 A:NXE1001 1.3 58.9 1.0 F12 A:NXE1001 2.1 47.5 1.0 F11 A:NXE1001 2.1 50.0 1.0 C7 A:NXE1001 2.4 61.5 1.0 N8 A:NXE1001 2.9 53.1 1.0 CG A:MET30 3.4 17.6 1.0 C6 A:NXE1001 3.6 49.1 1.0 CZ A:PHE26 3.7 49.8 1.0 CE1 A:PHE26 3.8 36.8 1.0 CD2 A:HIS29 3.9 3.6 1.0 O9 A:NXE1001 4.2 48.3 1.0 NE2 A:HIS29 4.2 3.8 1.0 CD1 A:LEU33 4.4 15.0 1.0 CA A:MET30 4.5 10.4 1.0 CB A:MET30 4.5 12.8 1.0 C5 A:NXE1001 4.5 49.0 1.0 SD A:MET30 4.5 28.6 1.0 CD B:LYS311 4.6 19.4 1.0 CE2 A:PHE26 4.7 49.3 1.0 O A:ALA388 4.7 5.7 1.0 N A:MET30 4.8 8.0 1.0 CD1 A:PHE26 4.9 34.5 1.0

Fluorine binding site 4 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:48.0 occ:1.00 F11 B:NXE1001 0.0 48.0 1.0 C10 B:NXE1001 1.3 59.1 1.0 F12 B:NXE1001 2.1 49.0 1.0 F13 B:NXE1001 2.1 62.8 1.0 C7 B:NXE1001 2.4 60.6 1.0 C6 B:NXE1001 2.9 48.7 1.0 O B:ALA388 3.3 5.7 1.0 NE2 B:HIS29 3.5 3.8 1.0 C1 B:DMS1003 3.5 36.9 1.0 N8 B:NXE1001 3.6 50.8 1.0 CE1 B:PHE26 3.7 37.5 1.0 CD2 B:HIS29 3.7 3.6 1.0 CZ B:PHE26 4.0 50.9 1.0 C5 B:NXE1001 4.3 49.3 1.0 C B:ALA388 4.4 6.7 1.0 O9 B:NXE1001 4.6 46.0 1.0 N B:TYR390 4.6 4.0 1.0 CD2 B:LEU353 4.7 9.4 1.0 CB B:TYR390 4.7 0.8 1.0 CD1 B:PHE26 4.8 34.6 1.0 CE1 B:HIS29 4.8 3.7 1.0 CD1 B:LEU353 5.0 10.9 1.0 CA B:ILE389 5.0 5.3 1.0

Fluorine binding site 5 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:49.0 occ:1.00 F12 B:NXE1001 0.0 49.0 1.0 C10 B:NXE1001 1.3 59.1 1.0 F13 B:NXE1001 2.1 62.8 1.0 F11 B:NXE1001 2.1 48.0 1.0 C7 B:NXE1001 2.4 60.6 1.0 N8 B:NXE1001 3.0 50.8 1.0 C6 B:NXE1001 3.5 48.7 1.0 CD1 B:LEU353 3.7 10.9 1.0 O B:ALA388 3.8 5.7 1.0 CD A:LYS311 3.8 19.6 1.0 CD2 B:LEU353 4.2 9.4 1.0 CD1 B:LEU33 4.2 15.1 1.0 O9 B:NXE1001 4.3 46.0 1.0 CB B:ALA388 4.3 8.2 1.0 C5 B:NXE1001 4.5 49.3 1.0 CG B:LEU353 4.6 9.5 1.0 CE A:LYS311 4.6 31.1 1.0 C B:ALA388 4.7 6.7 1.0 NE2 B:HIS29 4.7 3.8 1.0 CG A:LYS311 4.9 15.6 1.0 NZ A:LYS311 5.0 26.4 1.0

Fluorine binding site 6 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:62.8 occ:1.00 F13 B:NXE1001 0.0 62.8 1.0 C10 B:NXE1001 1.3 59.1 1.0 F12 B:NXE1001 2.1 49.0 1.0 F11 B:NXE1001 2.1 48.0 1.0 C7 B:NXE1001 2.4 60.6 1.0 N8 B:NXE1001 2.9 50.8 1.0 CG B:MET30 3.3 17.6 1.0 C6 B:NXE1001 3.6 48.7 1.0 CZ B:PHE26 3.7 50.9 1.0 CE1 B:PHE26 3.9 37.5 1.0 CD2 B:HIS29 4.1 3.6 1.0 O9 B:NXE1001 4.2 46.0 1.0 CD1 B:LEU33 4.4 15.1 1.0 NE2 B:HIS29 4.4 3.8 1.0 SD B:MET30 4.5 28.4 1.0 CD A:LYS311 4.5 19.6 1.0 CB B:MET30 4.5 12.8 1.0 CA B:MET30 4.5 10.4 1.0 C5 B:NXE1001 4.5 49.3 1.0 CE2 B:PHE26 4.7 50.2 1.0 O B:ALA388 4.9 5.7 1.0 N B:MET30 4.9 8.0 1.0 CG A:LYS311 4.9 15.6 1.0 CD1 B:PHE26 5.0 34.6 1.0

Fluorine binding site 7 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:48.7 occ:1.00 F11 C:NXE1001 0.0 48.7 1.0 C10 C:NXE1001 1.3 59.2 1.0 F12 C:NXE1001 2.1 48.3 1.0 F13 C:NXE1001 2.1 62.6 1.0 C7 C:NXE1001 2.4 60.8 1.0 C6 C:NXE1001 2.9 48.8 1.0 O C:ALA388 3.3 5.8 1.0 NE2 C:HIS29 3.5 3.8 1.0 C1 C:DMS1003 3.5 36.7 1.0 N8 C:NXE1001 3.6 51.5 1.0 CE1 C:PHE26 3.6 37.1 1.0 CD2 C:HIS29 3.7 3.6 1.0 CZ C:PHE26 3.9 50.6 1.0 C5 C:NXE1001 4.3 49.6 1.0 C C:ALA388 4.5 6.8 1.0 O9 C:NXE1001 4.6 46.5 1.0 N C:TYR390 4.6 4.0 1.0 CB C:TYR390 4.7 1.0 1.0 CD2 C:LEU353 4.7 9.3 1.0 CD1 C:PHE26 4.8 34.3 1.0 CE1 C:HIS29 4.8 3.7 1.0 CA C:ILE389 5.0 5.3 1.0 CD1 C:LEU353 5.0 10.8 1.0

Fluorine binding site 8 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:48.3 occ:1.00 F12 C:NXE1001 0.0 48.3 1.0 C10 C:NXE1001 1.3 59.2 1.0 F11 C:NXE1001 2.1 48.7 1.0 F13 C:NXE1001 2.1 62.6 1.0 C7 C:NXE1001 2.4 60.8 1.0 N8 C:NXE1001 3.1 51.5 1.0 C6 C:NXE1001 3.5 48.8 1.0 CD1 C:LEU353 3.7 10.8 1.0 O C:ALA388 3.8 5.8 1.0 CD D:LYS311 3.9 19.6 1.0 CD2 C:LEU353 4.1 9.3 1.0 CD1 C:LEU33 4.3 15.1 1.0 O9 C:NXE1001 4.3 46.5 1.0 CB C:ALA388 4.3 8.3 1.0 C5 C:NXE1001 4.5 49.6 1.0 CG C:LEU353 4.5 9.4 1.0 C C:ALA388 4.6 6.8 1.0 NE2 C:HIS29 4.7 3.8 1.0 CE D:LYS311 4.7 31.1 1.0 CG D:LYS311 4.9 15.6 1.0 NZ D:LYS311 5.0 26.2 1.0 CD2 C:HIS29 5.0 3.6 1.0

Fluorine binding site 9 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:62.6 occ:1.00 F13 C:NXE1001 0.0 62.6 1.0 C10 C:NXE1001 1.3 59.2 1.0 F12 C:NXE1001 2.1 48.3 1.0 F11 C:NXE1001 2.1 48.7 1.0 C7 C:NXE1001 2.4 60.8 1.0 N8 C:NXE1001 2.9 51.5 1.0 CG C:MET30 3.3 17.5 1.0 C6 C:NXE1001 3.6 48.8 1.0 CZ C:PHE26 3.7 50.6 1.0 CE1 C:PHE26 3.9 37.1 1.0 CD2 C:HIS29 4.1 3.6 1.0 O9 C:NXE1001 4.2 46.5 1.0 CD1 C:LEU33 4.4 15.1 1.0 NE2 C:HIS29 4.4 3.8 1.0 CD D:LYS311 4.4 19.6 1.0 SD C:MET30 4.5 28.4 1.0 CB C:MET30 4.5 12.8 1.0 CA C:MET30 4.5 10.4 1.0 C5 C:NXE1001 4.5 49.6 1.0 CE2 C:PHE26 4.7 50.1 1.0 O C:ALA388 4.9 5.8 1.0 N C:MET30 4.9 7.9 1.0 CG D:LYS311 4.9 15.6 1.0 CD1 C:PHE26 5.0 34.3 1.0

Fluorine binding site 10 out of 12 in the PKM2 in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of PKM2 in Complex with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1001 b:52.4 occ:1.00 F11 D:NXE1001 0.0 52.4 1.0 C10 D:NXE1001 1.3 60.3 1.0 F12 D:NXE1001 2.1 51.4 1.0 F13 D:NXE1001 2.1 66.1 1.0 C7 D:NXE1001 2.4 64.0 1.0 C6 D:NXE1001 2.9 51.4 1.0 O D:ALA388 3.3 5.7 1.0 C1 D:DMS1003 3.3 36.3 1.0 NE2 D:HIS29 3.5 3.8 1.0 N8 D:NXE1001 3.6 55.6 1.0 CE1 D:PHE26 3.6 37.2 1.0 CD2 D:HIS29 3.7 3.6 1.0 CZ D:PHE26 4.0 50.3 1.0 C5 D:NXE1001 4.2 50.0 1.0 C D:ALA388 4.4 6.8 1.0 N D:TYR390 4.5 4.0 1.0 O9 D:NXE1001 4.5 49.6 1.0 CB D:TYR390 4.6 0.8 1.0 CD2 D:LEU353 4.6 9.2 1.0 CD1 D:PHE26 4.8 34.2 1.0 CE1 D:HIS29 4.8 3.7 1.0 CA D:ILE389 4.9 5.3 1.0 S D:DMS1003 4.9 34.6 1.0 C D:ILE389 4.9 4.5 1.0

M.Saur, M.J.Hartshorn, J.Dong, J.Reeks, G.Bunkoczi, H.Jhoti, P.A.Williams. Fragment-Based Drug Discovery Using Cryo-Em. Drug Discov Today 2019.
ISSN: ESSN 1878-5832
PubMed: 31877353
DOI: 10.1016/J.DRUDIS.2019.12.006