Fluorine in PDB 9d02: Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine

The structure of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine, PDB code: 9d02 was solved by S.L.Delker, T.E.Edwards, J.Abendroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.71 / 2.15
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	60.43, 60.43, 317.71, 90, 90, 120
R / Rfree (%)	15.7 / 19.5

The structure of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Fluorine atom in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine (pdb code 9d02). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine, PDB code: 9d02:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:48.9 occ:0.88 F01 A:R1J403 0.0 48.9 0.9 C02 A:R1J403 1.4 49.3 0.9 C03 A:R1J403 2.4 40.8 0.9 C24 A:R1J403 2.4 55.0 0.9 O25 A:R1J403 2.8 69.7 0.9 CB A:CYS146 3.1 37.8 1.0 O A:GLY197 3.2 41.0 1.0 CG A:TYR209 3.6 52.6 1.0 C04 A:R1J403 3.6 46.6 0.9 C23 A:R1J403 3.6 53.8 0.9 F28 A:R1J403 3.6 71.2 0.9 N A:CYS146 3.7 43.8 1.0 C A:ALA196 3.7 40.0 1.0 C26 A:R1J403 3.7 72.0 0.9 N A:GLY197 3.7 38.1 1.0 CD2 A:TYR209 3.8 52.6 1.0 O A:ALA196 3.8 50.4 1.0 C A:GLY197 3.8 42.9 1.0 CD1 A:TYR209 3.9 49.5 1.0 CB A:ALA196 3.9 39.2 1.0 CA A:CYS146 4.0 36.4 1.0 CB A:TYR209 4.0 47.2 1.0 CA A:GLY197 4.0 38.1 1.0 C22 A:R1J403 4.1 49.1 0.9 CE2 A:TYR209 4.3 54.1 1.0 CA A:ALA196 4.3 39.4 1.0 CE1 A:TYR209 4.3 50.3 1.0 F27 A:R1J403 4.4 73.2 0.9 CZ A:TYR209 4.5 51.9 1.0 SG A:CYS146 4.5 48.6 1.0 O A:CYS146 4.6 37.7 1.0 C A:MET145 4.7 43.4 1.0 N A:ALA196 4.7 32.5 1.0 F29 A:R1J403 4.8 69.9 0.9 C A:CYS146 4.8 44.0 1.0 C05 A:R1J403 4.9 43.3 0.9 N A:ALA198 5.0 41.3 1.0 CA A:MET145 5.0 39.0 1.0

Fluorine binding site 2 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:73.2 occ:0.88 F27 A:R1J403 0.0 73.2 0.9 C26 A:R1J403 1.3 72.0 0.9 F28 A:R1J403 2.1 71.2 0.9 F29 A:R1J403 2.2 69.9 0.9 O25 A:R1J403 2.2 69.7 0.9 CD1 A:ILE161 3.2 68.2 1.0 CG2 A:ILE161 3.2 49.4 1.0 CG1 A:ILE161 3.4 60.7 1.0 C24 A:R1J403 3.6 55.0 0.9 CB A:SER144 3.8 40.5 1.0 CB A:ILE161 3.9 56.1 1.0 CB A:CYS146 4.1 37.8 1.0 ND1 A:HIS201 4.2 67.9 1.0 C A:MET145 4.3 43.4 1.0 O A:MET145 4.3 39.3 1.0 N A:CYS146 4.3 43.8 1.0 C23 A:R1J403 4.3 53.8 0.9 F01 A:R1J403 4.4 48.9 0.9 N A:MET145 4.4 45.9 1.0 OG A:SER144 4.4 55.8 1.0 C02 A:R1J403 4.4 49.3 0.9 CE1 A:HIS201 4.5 73.3 1.0 CA A:CYS146 4.5 36.4 1.0 CA A:ILE161 4.6 47.5 1.0 CA A:MET145 4.8 39.0 1.0 C A:SER144 4.9 45.1 1.0 CA A:SER144 4.9 38.4 1.0

Fluorine binding site 3 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:71.2 occ:0.88 F28 A:R1J403 0.0 71.2 0.9 C26 A:R1J403 1.3 72.0 0.9 F29 A:R1J403 2.1 69.9 0.9 F27 A:R1J403 2.1 73.2 0.9 O25 A:R1J403 2.2 69.7 0.9 C24 A:R1J403 2.8 55.0 0.9 CD2 A:TYR209 3.1 52.6 1.0 C02 A:R1J403 3.5 49.3 0.9 C23 A:R1J403 3.5 53.8 0.9 F01 A:R1J403 3.6 48.9 0.9 CE2 A:TYR209 3.7 54.1 1.0 CD1 A:ILE161 3.8 68.2 1.0 CG A:TYR209 4.0 52.6 1.0 CB A:TYR209 4.2 47.2 1.0 CA A:ALA206 4.2 58.6 1.0 CB A:CYS146 4.4 37.8 1.0 O A:SER202 4.4 72.1 1.0 C03 A:R1J403 4.5 40.8 0.9 CB A:ALA206 4.6 61.0 1.0 C22 A:R1J403 4.6 49.1 0.9 CG1 A:ILE161 4.6 60.7 1.0 N A:SER202 4.7 68.3 1.0 CZ A:TYR209 4.9 51.9 1.0 N A:ALA206 4.9 64.3 1.0

Fluorine binding site 4 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:69.9 occ:0.88 F29 A:R1J403 0.0 69.9 0.9 C26 A:R1J403 1.3 72.0 0.9 F28 A:R1J403 2.1 71.2 0.9 F27 A:R1J403 2.2 73.2 0.9 O25 A:R1J403 2.3 69.7 0.9 C24 A:R1J403 3.0 55.0 0.9 C23 A:R1J403 3.1 53.8 0.9 N A:SER202 3.4 68.3 1.0 CA A:HIS201 3.6 55.9 1.0 CB A:SER144 3.6 40.5 1.0 O A:TYR200 3.6 56.9 1.0 ND1 A:HIS201 3.6 67.9 1.0 C A:HIS201 4.0 64.5 1.0 OG A:SER144 4.1 55.8 1.0 C02 A:R1J403 4.2 49.3 0.9 CG A:HIS201 4.3 66.3 1.0 C22 A:R1J403 4.3 49.1 0.9 CE1 A:HIS201 4.4 73.3 1.0 O A:SER202 4.4 72.1 1.0 C A:TYR200 4.4 55.2 1.0 N A:HIS201 4.4 53.4 1.0 CA A:SER202 4.5 72.9 1.0 CB A:HIS201 4.5 57.0 1.0 CB A:SER202 4.6 81.1 1.0 CD1 A:ILE161 4.7 68.2 1.0 C A:SER202 4.8 71.2 1.0 F01 A:R1J403 4.8 48.9 0.9 CG2 A:ILE161 4.9 49.4 1.0 CD2 A:TYR209 4.9 52.6 1.0 CA A:SER144 5.0 38.4 1.0

Fluorine binding site 5 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:59.2 occ:0.95 F01 B:R1J403 0.0 59.2 0.9 C02 B:R1J403 1.4 61.8 0.9 C03 B:R1J403 2.3 62.4 0.9 C24 B:R1J403 2.4 60.7 0.9 O25 B:R1J403 2.8 73.3 0.9 CB B:CYS146 3.2 49.9 1.0 F28 B:R1J403 3.2 79.2 0.9 O B:GLY197 3.3 49.9 1.0 C26 B:R1J403 3.5 79.8 0.9 N B:CYS146 3.6 52.4 1.0 C04 B:R1J403 3.6 59.7 0.9 C23 B:R1J403 3.6 56.2 0.9 CG B:TYR209 3.6 58.9 1.0 C B:ALA196 3.7 45.5 1.0 N B:GLY197 3.7 47.3 1.0 CD2 B:TYR209 3.8 66.3 1.0 CB B:ALA196 3.9 39.0 1.0 CD1 B:TYR209 3.9 54.8 1.0 O B:ALA196 3.9 47.1 1.0 C B:GLY197 3.9 46.3 1.0 CA B:CYS146 4.0 51.5 1.0 CB B:TYR209 4.0 56.7 1.0 CA B:GLY197 4.0 44.7 1.0 C22 B:R1J403 4.1 55.1 0.9 CE2 B:TYR209 4.2 67.4 1.0 F27 B:R1J403 4.3 82.7 0.9 CE1 B:TYR209 4.3 54.7 1.0 CA B:ALA196 4.3 36.9 1.0 CZ B:TYR209 4.5 67.6 1.0 O B:CYS146 4.6 45.7 1.0 C B:MET145 4.6 55.1 1.0 F29 B:R1J403 4.6 80.4 0.9 N B:ALA196 4.7 47.2 1.0 SG B:CYS146 4.7 54.0 1.0 C B:CYS146 4.8 47.6 1.0 C05 B:R1J403 4.8 57.7 0.9 CA B:MET145 4.9 54.2 1.0 N B:ALA198 5.0 47.2 1.0

Fluorine binding site 6 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:82.7 occ:0.95 F27 B:R1J403 0.0 82.7 0.9 C26 B:R1J403 1.3 79.8 0.9 F29 B:R1J403 2.1 80.4 0.9 F28 B:R1J403 2.2 79.2 0.9 O25 B:R1J403 2.2 73.3 0.9 CG2 B:ILE161 3.3 68.4 1.0 OG B:SER144 3.3 78.7 1.0 CD1 B:ILE161 3.4 76.8 1.0 CG1 B:ILE161 3.5 70.7 1.0 C24 B:R1J403 3.6 60.7 0.9 CB B:SER144 3.7 67.8 1.0 C B:MET145 3.8 55.1 1.0 N B:CYS146 3.9 52.4 1.0 CB B:ILE161 3.9 70.7 1.0 N B:MET145 4.0 54.2 1.0 O B:MET145 4.0 60.9 1.0 CB B:CYS146 4.0 49.9 1.0 CA B:CYS146 4.3 51.5 1.0 F01 B:R1J403 4.3 59.2 0.9 CA B:MET145 4.3 54.2 1.0 C02 B:R1J403 4.4 61.8 0.9 C23 B:R1J403 4.4 56.2 0.9 C B:SER144 4.5 62.4 1.0 CA B:ILE161 4.5 63.5 1.0 CD2 B:HIS201 4.6 68.4 1.0 CA B:SER144 4.7 58.8 1.0 O B:SER162 5.0 60.6 1.0

Fluorine binding site 7 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:79.2 occ:0.95 F28 B:R1J403 0.0 79.2 0.9 C26 B:R1J403 1.3 79.8 0.9 F29 B:R1J403 2.2 80.4 0.9 F27 B:R1J403 2.2 82.7 0.9 O25 B:R1J403 2.2 73.3 0.9 C24 B:R1J403 2.8 60.7 0.9 CD2 B:TYR209 3.1 66.3 1.0 C02 B:R1J403 3.2 61.8 0.9 F01 B:R1J403 3.2 59.2 0.9 C23 B:R1J403 3.7 56.2 0.9 CG B:TYR209 3.8 58.9 1.0 CE2 B:TYR209 3.8 67.4 1.0 CD1 B:ILE161 3.9 76.8 1.0 CB B:TYR209 3.9 56.7 1.0 CB B:CYS146 4.0 49.9 1.0 C03 B:R1J403 4.3 62.4 0.9 CG1 B:ILE161 4.5 70.7 1.0 OG B:SER144 4.5 78.7 1.0 CA B:ALA206 4.6 73.5 1.0 C22 B:R1J403 4.7 55.1 0.9 N B:CYS146 4.7 52.4 1.0 CB B:ALA206 4.8 74.4 1.0 O B:SER202 4.8 68.7 1.0 CA B:CYS146 4.9 51.5 1.0 CD1 B:TYR209 4.9 54.8 1.0 CZ B:TYR209 4.9 67.6 1.0 C04 B:R1J403 5.0 59.7 0.9 SG B:CYS146 5.0 54.0 1.0

Fluorine binding site 8 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014883 (2R)-4-(Ethenesulfonyl)-1-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}-2-[(Prop-2-Yn-1-Yloxy) Methyl]Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:80.4 occ:0.95 F29 B:R1J403 0.0 80.4 0.9 C26 B:R1J403 1.3 79.8 0.9 F27 B:R1J403 2.1 82.7 0.9 F28 B:R1J403 2.2 79.2 0.9 O25 B:R1J403 2.3 73.3 0.9 OG B:SER144 2.7 78.7 1.0 C24 B:R1J403 3.0 60.7 0.9 C23 B:R1J403 3.2 56.2 0.9 N B:SER202 3.5 73.2 1.0 O B:TYR200 3.7 74.0 1.0 CB B:SER144 3.8 67.8 1.0 CA B:HIS201 3.8 73.3 1.0 CD2 B:HIS201 4.1 68.4 1.0 C B:HIS201 4.1 72.5 1.0 C02 B:R1J403 4.1 61.8 0.9 O B:SER202 4.3 68.7 1.0 C22 B:R1J403 4.5 55.1 0.9 CA B:SER202 4.5 75.6 1.0 CB B:SER202 4.5 74.5 1.0 C B:TYR200 4.5 74.3 1.0 CG B:HIS201 4.5 73.2 1.0 CD1 B:ILE161 4.6 76.8 1.0 N B:HIS201 4.6 77.0 1.0 F01 B:R1J403 4.6 59.2 0.9 CB B:HIS201 4.7 74.3 1.0 C B:SER202 4.8 74.3 1.0 CG2 B:ILE161 4.8 68.4 1.0 CD2 B:TYR209 4.8 66.3 1.0 NE2 B:HIS201 4.8 70.1 1.0 C B:SER144 4.9 62.4 1.0 CA B:SER144 5.0 58.8 1.0 N B:MET145 5.0 54.2 1.0

S.L.Delker, T.E.Edwards, J.Abendroth. Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC994967 1-(Ethenesulfonyl)-4-{[4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine To Be Published.