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Fluorine in PDB 9d03: Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine

Protein crystallography data

The structure of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine, PDB code: 9d03 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) 46.83 / 2.45
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 60.33, 60.33, 316.67, 90, 90, 120
R / Rfree (%) 15.9 / 20.1

Other elements in 9d03:

The structure of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine (pdb code 9d03). 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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine, PDB code: 9d03:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 9d03

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Fluorine binding site 1 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:35.4
occ:0.65
 F01 A:R1M403 0.0 35.4 0.7
C02 A:R1M403 1.3 36.1 0.7
C03 A:R1M403 2.3 39.8 0.7
C19 A:R1M403 2.3 37.6 0.7
F24 A:R1M403 2.7 46.5 0.7
O20 A:R1M403 2.8 43.2 0.7
CB A:CYS146 3.2 43.8 1.0
C21 A:R1M403 3.2 48.0 0.7
O A:GLY197 3.3 43.1 1.0
C04 A:R1M403 3.6 42.3 0.7
C18 A:R1M403 3.6 39.7 0.7
CG A:TYR209 3.6 59.1 1.0
CD2 A:TYR209 3.7 56.8 1.0
N A:CYS146 3.8 46.7 1.0
C A:ALA196 3.9 48.0 1.0
N A:GLY197 4.0 44.9 1.0
O A:ALA196 4.0 50.5 1.0
CD1 A:TYR209 4.0 62.9 1.0
F23 A:R1M403 4.0 49.1 0.7
CB A:TYR209 4.0 49.8 1.0
C A:GLY197 4.0 43.4 1.0
CA A:CYS146 4.1 44.0 1.0
C17 A:R1M403 4.1 38.7 0.7
CE2 A:TYR209 4.1 60.4 1.0
CB A:ALA196 4.1 41.0 1.0
CA A:GLY197 4.3 37.9 1.0
F22 A:R1M403 4.3 46.3 0.7
CE1 A:TYR209 4.4 62.9 1.0
CZ A:TYR209 4.4 61.8 1.0
CA A:ALA196 4.5 44.8 1.0
SG A:CYS146 4.6 57.0 1.0
C A:MET145 4.7 43.2 1.0
O A:CYS146 4.8 46.7 1.0
C05 A:R1M403 4.8 48.2 0.7
C A:CYS146 4.9 44.5 1.0
N A:ALA196 5.0 41.7 1.0

Fluorine binding site 2 out of 8 in 9d03

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Fluorine binding site 2 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:46.3
occ:0.65
 F22 A:R1M403 0.0 46.3 0.7
C21 A:R1M403 1.3 48.0 0.7
F24 A:R1M403 2.2 46.5 0.7
F23 A:R1M403 2.2 49.1 0.7
O20 A:R1M403 2.2 43.2 0.7
C19 A:R1M403 3.0 37.6 0.7
OG A:SER144 3.1 73.7 1.0
C18 A:R1M403 3.4 39.7 0.7
N A:SER202 3.7 85.5 1.0
CD2 A:HIS201 3.8 89.5 1.0
O A:TYR200 3.9 64.0 1.0
C02 A:R1M403 4.0 36.1 0.7
CA A:HIS201 4.1 79.1 1.0
CB A:SER144 4.2 66.5 1.0
F01 A:R1M403 4.3 35.4 0.7
C A:HIS201 4.4 81.5 1.0
O A:SER202 4.4 98.5 1.0
CD1 A:ILE161 4.5 76.6 1.0
CD2 A:TYR209 4.5 56.8 1.0
NE2 A:HIS201 4.6 94.5 1.0
CG A:HIS201 4.6 92.2 1.0
C17 A:R1M403 4.6 38.7 0.7
CA A:SER202 4.6 95.1 1.0
C A:TYR200 4.7 67.6 1.0
C A:SER202 4.8 93.8 1.0
CB A:SER202 4.8 94.1 1.0
N A:HIS201 4.8 72.2 1.0
CE2 A:TYR209 4.8 60.4 1.0
CG2 A:ILE161 4.9 52.0 1.0
CB A:HIS201 4.9 84.7 1.0

Fluorine binding site 3 out of 8 in 9d03

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Fluorine binding site 3 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:49.1
occ:0.65
 F23 A:R1M403 0.0 49.1 0.7
C21 A:R1M403 1.3 48.0 0.7
F24 A:R1M403 2.2 46.5 0.7
F22 A:R1M403 2.2 46.3 0.7
O20 A:R1M403 2.2 43.2 0.7
OG A:SER144 2.9 73.7 1.0
CG2 A:ILE161 3.4 52.0 1.0
C19 A:R1M403 3.5 37.6 0.7
C A:MET145 3.6 43.2 1.0
CD1 A:ILE161 3.7 76.6 1.0
CB A:SER144 3.7 66.5 1.0
N A:MET145 3.7 49.2 1.0
N A:CYS146 3.8 46.7 1.0
CG1 A:ILE161 3.8 66.3 1.0
O A:MET145 3.8 50.7 1.0
CB A:CYS146 3.9 43.8 1.0
F01 A:R1M403 4.0 35.4 0.7
CA A:MET145 4.0 44.7 1.0
CB A:ILE161 4.1 57.6 1.0
CA A:CYS146 4.1 44.0 1.0
C02 A:R1M403 4.2 36.1 0.7
C A:SER144 4.3 52.2 1.0
CD2 A:HIS201 4.4 89.5 1.0
C18 A:R1M403 4.5 39.7 0.7
CA A:ILE161 4.6 47.3 1.0
CA A:SER144 4.6 57.0 1.0
O A:SER144 5.0 51.7 1.0
NE2 A:HIS201 5.0 94.5 1.0

Fluorine binding site 4 out of 8 in 9d03

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Fluorine binding site 4 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:46.5
occ:0.65
 F24 A:R1M403 0.0 46.5 0.7
C21 A:R1M403 1.3 48.0 0.7
F23 A:R1M403 2.2 49.1 0.7
F22 A:R1M403 2.2 46.3 0.7
O20 A:R1M403 2.2 43.2 0.7
F01 A:R1M403 2.7 35.4 0.7
C19 A:R1M403 2.8 37.6 0.7
C02 A:R1M403 3.0 36.1 0.7
CD2 A:TYR209 3.3 56.8 1.0
CB A:CYS146 3.4 43.8 1.0
CG A:TYR209 3.8 59.1 1.0
C18 A:R1M403 3.9 39.7 0.7
CB A:TYR209 3.9 49.8 1.0
CE2 A:TYR209 4.0 60.4 1.0
CD1 A:ILE161 4.1 76.6 1.0
C03 A:R1M403 4.2 39.8 0.7
N A:CYS146 4.3 46.7 1.0
CA A:CYS146 4.4 44.0 1.0
SG A:CYS146 4.5 57.0 1.0
OG A:SER144 4.5 73.7 1.0
CG1 A:ILE161 4.5 66.3 1.0
C A:MET145 4.8 43.2 1.0
C17 A:R1M403 4.9 38.7 0.7
CD1 A:TYR209 4.9 62.9 1.0
C04 A:R1M403 5.0 42.3 0.7

Fluorine binding site 5 out of 8 in 9d03

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Fluorine binding site 5 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:49.3
occ:0.65
 F01 B:R1M403 0.0 49.3 0.7
C02 B:R1M403 1.4 42.9 0.7
C19 B:R1M403 2.3 45.7 0.7
C03 B:R1M403 2.4 38.0 0.7
O20 B:R1M403 2.7 55.4 0.7
O B:GLY197 3.1 60.3 1.0
CB B:CYS146 3.4 57.8 1.0
C B:ALA196 3.4 48.2 1.0
CB B:ALA196 3.5 55.2 1.0
N B:GLY197 3.5 47.1 1.0
C18 B:R1M403 3.6 42.0 0.7
O B:ALA196 3.6 53.9 1.0
C04 B:R1M403 3.6 39.4 0.7
CG B:TYR209 3.7 67.4 1.0
C21 B:R1M403 3.7 53.9 0.7
C B:GLY197 3.8 53.1 1.0
CD1 B:TYR209 3.8 65.4 1.0
N B:CYS146 3.8 47.9 1.0
CA B:GLY197 3.9 48.7 1.0
CD2 B:TYR209 3.9 75.3 1.0
CA B:ALA196 3.9 46.4 1.0
F22 B:R1M403 4.0 56.7 0.7
F24 B:R1M403 4.0 52.3 0.7
C17 B:R1M403 4.1 37.1 0.7
CB B:TYR209 4.1 65.1 1.0
CA B:CYS146 4.2 50.9 1.0
CE1 B:TYR209 4.2 65.3 1.0
CE2 B:TYR209 4.3 74.5 1.0
CZ B:TYR209 4.4 73.4 1.0
N B:ALA196 4.4 44.5 1.0
O B:CYS146 4.5 47.1 1.0
SG B:CYS146 4.8 65.1 1.0
C B:MET145 4.9 53.5 1.0
C B:CYS146 4.9 48.2 1.0
N B:ALA198 4.9 51.4 1.0
F23 B:R1M403 4.9 49.0 0.7
C05 B:R1M403 4.9 43.6 0.7

Fluorine binding site 6 out of 8 in 9d03

Go back to Fluorine Binding Sites List in 9d03
Fluorine binding site 6 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:56.7
occ:0.65
 F22 B:R1M403 0.0 56.7 0.7
C21 B:R1M403 1.3 53.9 0.7
F23 B:R1M403 2.1 49.0 0.7
F24 B:R1M403 2.2 52.3 0.7
O20 B:R1M403 2.2 55.4 0.7
C19 B:R1M403 2.6 45.7 0.7
C18 B:R1M403 2.9 42.0 0.7
CD2 B:TYR209 3.2 75.3 1.0
C02 B:R1M403 3.5 42.9 0.7
CE2 B:TYR209 3.6 74.5 1.0
OG B:SER144 3.9 87.8 1.0
F01 B:R1M403 4.0 49.3 0.7
C17 B:R1M403 4.0 37.1 0.7
CG B:TYR209 4.2 67.4 1.0
N B:SER202 4.4 87.3 1.0
CD1 B:ILE161 4.4 79.1 1.0
C03 B:R1M403 4.5 38.0 0.7
ND1 B:HIS201 4.5 113.4 1.0
O B:SER202 4.6 99.3 1.0
CB B:TYR209 4.6 65.1 1.0
C04 B:R1M403 4.7 39.4 0.7
O B:TYR200 4.7 77.2 1.0
CZ B:TYR209 4.8 73.4 1.0
CB B:CYS146 4.8 57.8 1.0
CB B:SER202 4.9 106.0 1.0
CE1 B:HIS201 5.0 112.4 1.0

Fluorine binding site 7 out of 8 in 9d03

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Fluorine binding site 7 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:49.0
occ:0.65
 F23 B:R1M403 0.0 49.0 0.7
C21 B:R1M403 1.3 53.9 0.7
OG B:SER144 2.0 87.8 1.0
F22 B:R1M403 2.1 56.7 0.7
F24 B:R1M403 2.1 52.3 0.7
O20 B:R1M403 2.3 55.4 0.7
CB B:SER144 3.0 74.7 1.0
C19 B:R1M403 3.3 45.7 0.7
C18 B:R1M403 3.5 42.0 0.7
ND1 B:HIS201 3.6 113.4 1.0
N B:MET145 3.8 59.2 1.0
CG2 B:ILE161 3.9 62.9 1.0
C B:SER144 3.9 66.1 1.0
CE1 B:HIS201 4.0 112.4 1.0
CA B:SER144 4.1 68.9 1.0
CA B:HIS201 4.2 94.2 1.0
CG B:HIS201 4.3 115.2 1.0
CA B:MET145 4.4 52.5 1.0
C B:MET145 4.5 53.5 1.0
CD1 B:ILE161 4.5 79.1 1.0
O B:SER144 4.5 64.2 1.0
C02 B:R1M403 4.5 42.9 0.7
N B:SER202 4.6 87.3 1.0
O B:TYR200 4.6 77.2 1.0
N B:CYS146 4.7 47.9 1.0
CB B:HIS201 4.8 108.8 1.0
NE2 B:HIS201 4.8 113.8 1.0
CG1 B:ILE161 4.8 72.1 1.0
C17 B:R1M403 4.9 37.1 0.7
O B:MET145 4.9 56.1 1.0
F01 B:R1M403 4.9 49.3 0.7
CB B:ILE161 5.0 65.1 1.0
N B:HIS201 5.0 90.2 1.0
C B:HIS201 5.0 88.9 1.0

Fluorine binding site 8 out of 8 in 9d03

Go back to Fluorine Binding Sites List in 9d03
Fluorine binding site 8 out of 8 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]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 SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:52.3
occ:0.65
 F24 B:R1M403 0.0 52.3 0.7
C21 B:R1M403 1.3 53.9 0.7
F23 B:R1M403 2.1 49.0 0.7
F22 B:R1M403 2.2 56.7 0.7
O20 B:R1M403 2.3 55.4 0.7
CD1 B:ILE161 3.2 79.1 1.0
CB B:CYS146 3.2 57.8 1.0
CG1 B:ILE161 3.3 72.1 1.0
C19 B:R1M403 3.4 45.7 0.7
CG2 B:ILE161 3.6 62.9 1.0
N B:CYS146 3.7 47.9 1.0
CA B:CYS146 3.8 50.9 1.0
C B:MET145 3.9 53.5 1.0
F01 B:R1M403 4.0 49.3 0.7
OG B:SER144 4.0 87.8 1.0
CB B:ILE161 4.0 65.1 1.0
C02 B:R1M403 4.2 42.9 0.7
O B:MET145 4.3 56.1 1.0
C18 B:R1M403 4.3 42.0 0.7
SG B:CYS146 4.4 65.1 1.0
CD2 B:TYR209 4.4 75.3 1.0
N B:MET145 4.5 59.2 1.0
CA B:MET145 4.5 52.5 1.0
CA B:ILE161 4.6 58.2 1.0
CB B:TYR209 4.6 65.1 1.0
CB B:SER144 4.8 74.7 1.0
CG B:TYR209 4.8 67.4 1.0
CE1 B:HIS201 4.9 112.4 1.0
ND1 B:HIS201 5.0 113.4 1.0

Reference:

S.L.Delker, T.E.Edwards, J.Abendroth. Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4-(Trifluoromethoxy) Phenyl]Methyl}Piperazine To Be Published.
Page generated: Sat Aug 23 01:54:19 2025

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