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Fluorine in PDB 6blf: PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid

Enzymatic activity of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid

All present enzymatic activity of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid:
3.1.4.17;

Protein crystallography data

The structure of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid, PDB code: 6blf was solved by H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.030, 95.830, 104.130, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.8

Other elements in 6blf:

The structure of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid (pdb code 6blf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid, PDB code: 6blf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6blf

Go back to Fluorine Binding Sites List in 6blf
Fluorine binding site 1 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:28.1
occ:1.00
 F3 A:DY11000 0.0 28.1 1.0
C1 A:DY11000 1.4 26.2 1.0
C A:DY11000 2.3 23.5 1.0
C2 A:DY11000 2.3 25.3 1.0
OE1 A:GLN859 3.0 29.2 1.0
OH A:TYR827 3.2 27.1 1.0
CG A:PHE862 3.3 29.7 1.0
CD2 A:PHE862 3.3 32.7 1.0
CB A:PHE862 3.5 28.2 1.0
O A:HOH1103 3.5 26.8 1.0
C5 A:DY11000 3.6 25.1 1.0
C3 A:DY11000 3.6 25.2 1.0
O A:HOH1170 3.7 32.6 1.0
CD1 A:PHE862 3.9 32.6 1.0
CE2 A:PHE862 4.0 35.1 1.0
CZ A:TYR827 4.0 29.2 1.0
C4 A:DY11000 4.1 23.4 1.0
CD A:GLN859 4.1 33.9 1.0
O A:HOH1152 4.5 28.0 1.0
CE1 A:TYR827 4.5 26.2 1.0
CE1 A:PHE862 4.5 33.1 1.0
CZ A:PHE862 4.6 32.4 1.0
CG2 A:ILE826 4.7 21.2 1.0
O A:LEU858 4.7 23.3 1.0
C6 A:DY11000 4.9 26.9 1.0
C23 A:DY11000 4.9 29.9 1.0
NE2 A:GLN859 4.9 25.4 1.0
CE2 A:TYR827 4.9 22.6 1.0
CA A:GLN859 5.0 22.7 1.0

Fluorine binding site 2 out of 8 in 6blf

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Fluorine binding site 2 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:37.5
occ:1.00
 F2 A:DY11000 0.0 37.5 1.0
C16 A:DY11000 1.3 35.2 1.0
F A:DY11000 2.1 35.2 1.0
F1 A:DY11000 2.1 33.8 1.0
C13 A:DY11000 2.4 31.5 1.0
C12 A:DY11000 2.7 28.1 1.0
CD1 A:LEU770 3.3 32.8 1.0
C14 A:DY11000 3.6 29.2 1.0
CG2 A:ILE866 3.8 35.8 1.0
CD1 A:ILE870 4.1 34.4 1.0
CA A:LEU770 4.1 26.4 1.0
C11 A:DY11000 4.1 27.5 1.0
CB A:HIS773 4.2 31.2 1.0
CG A:HIS773 4.2 33.8 1.0
CB A:LEU770 4.3 25.4 1.0
CD2 A:HIS773 4.3 35.2 1.0
CG A:LEU770 4.4 30.1 1.0
CG2 A:THR805 4.4 22.1 1.0
CD1 A:LEU809 4.5 26.2 1.0
CB A:THR805 4.6 27.9 1.0
N A:LEU770 4.7 25.4 1.0
C15 A:DY11000 4.8 27.9 1.0
CD2 A:LEU809 4.9 29.8 1.0
C10 A:DY11000 5.0 28.5 1.0

Fluorine binding site 3 out of 8 in 6blf

Go back to Fluorine Binding Sites List in 6blf
Fluorine binding site 3 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:33.8
occ:1.00
 F1 A:DY11000 0.0 33.8 1.0
C16 A:DY11000 1.3 35.2 1.0
F A:DY11000 2.1 35.2 1.0
F2 A:DY11000 2.1 37.5 1.0
C13 A:DY11000 2.3 31.5 1.0
C14 A:DY11000 2.9 29.2 1.0
O A:THR768 3.2 22.0 1.0
C12 A:DY11000 3.5 28.1 1.0
C A:THR768 3.6 24.2 1.0
N A:LEU770 3.7 25.4 1.0
CG2 A:THR805 3.7 22.1 1.0
CA A:LEU770 3.8 26.4 1.0
C A:ASP769 3.8 27.2 1.0
O A:ASP769 4.0 27.5 1.0
O A:ALA767 4.1 24.5 1.0
CA A:THR768 4.1 20.6 1.0
C15 A:DY11000 4.2 27.9 1.0
N A:ASP769 4.2 21.2 1.0
CB A:HIS773 4.4 31.2 1.0
CB A:THR805 4.4 27.9 1.0
CB A:LEU770 4.5 25.4 1.0
O A:HOH1154 4.5 31.6 1.0
CA A:ASP769 4.5 22.3 1.0
CD1 A:LEU770 4.6 32.8 1.0
C11 A:DY11000 4.7 27.5 1.0
C A:ALA767 5.0 25.1 1.0
C A:LEU770 5.0 34.3 1.0
C10 A:DY11000 5.0 28.5 1.0

Fluorine binding site 4 out of 8 in 6blf

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Fluorine binding site 4 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:35.2
occ:1.00
 F A:DY11000 0.0 35.2 1.0
C16 A:DY11000 1.3 35.2 1.0
F2 A:DY11000 2.1 37.5 1.0
F1 A:DY11000 2.1 33.8 1.0
C13 A:DY11000 2.3 31.5 1.0
C14 A:DY11000 3.1 29.2 1.0
C12 A:DY11000 3.3 28.1 1.0
CB A:THR805 3.3 27.9 1.0
CG2 A:THR805 3.4 22.1 1.0
CA A:THR805 3.8 21.8 1.0
CG A:LEU809 3.9 26.1 1.0
O A:THR805 4.0 27.0 1.0
CD2 A:LEU809 4.0 29.8 1.0
CD1 A:LEU809 4.0 26.2 1.0
CD1 A:ILE870 4.2 34.4 1.0
C15 A:DY11000 4.3 27.9 1.0
C A:THR805 4.4 28.0 1.0
C11 A:DY11000 4.5 27.5 1.0
CB A:ASP808 4.5 21.0 1.0
OG1 A:THR805 4.6 31.1 1.0
O A:THR768 4.7 22.0 1.0
OD2 A:ASP808 4.7 26.9 1.0
C10 A:DY11000 4.9 28.5 1.0

Fluorine binding site 5 out of 8 in 6blf

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Fluorine binding site 5 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:30.5
occ:1.00
 F3 B:DY11000 0.0 30.5 1.0
C1 B:DY11000 1.4 29.2 1.0
C B:DY11000 2.3 27.1 1.0
C2 B:DY11000 2.3 29.5 1.0
NE2 B:GLN859 3.0 23.9 1.0
CG B:PHE862 3.4 29.2 1.0
OH B:TYR827 3.4 27.4 1.0
O B:HOH1145 3.5 28.1 1.0
CB B:PHE862 3.5 26.9 1.0
CD2 B:PHE862 3.5 31.4 1.0
O B:HOH1166 3.6 32.0 1.0
C5 B:DY11000 3.6 26.9 1.0
C3 B:DY11000 3.6 28.9 1.0
CD1 B:PHE862 3.9 32.3 1.0
C4 B:DY11000 4.1 26.1 1.0
CD B:GLN859 4.2 40.0 1.0
CE2 B:PHE862 4.2 33.7 1.0
CZ B:TYR827 4.2 29.4 1.0
O B:HOH1170 4.5 28.0 1.0
CE1 B:PHE862 4.5 32.7 1.0
O B:LEU858 4.6 29.7 1.0
CZ B:PHE862 4.7 31.3 1.0
CG2 B:ILE826 4.7 25.8 1.0
CE1 B:TYR827 4.8 25.4 1.0
OE1 B:GLN859 4.8 31.1 1.0
C6 B:DY11000 4.9 25.7 1.0
CA B:GLN859 4.9 24.7 1.0
C23 B:DY11000 4.9 31.4 1.0

Fluorine binding site 6 out of 8 in 6blf

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Fluorine binding site 6 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:38.6
occ:1.00
 F2 B:DY11000 0.0 38.6 1.0
C16 B:DY11000 1.3 33.4 1.0
F1 B:DY11000 2.1 33.6 1.0
F B:DY11000 2.1 31.7 1.0
C13 B:DY11000 2.3 27.1 1.0
C12 B:DY11000 2.7 24.9 1.0
CD1 B:LEU770 3.2 32.2 1.0
C14 B:DY11000 3.6 24.4 1.0
CG2 B:ILE866 4.0 23.9 1.0
C11 B:DY11000 4.1 25.0 1.0
CD1 B:ILE870 4.1 23.6 1.0
CA B:LEU770 4.2 25.8 1.0
CB B:LEU770 4.2 26.8 1.0
CB B:HIS773 4.2 25.3 1.0
CG B:LEU770 4.3 31.6 1.0
CD2 B:HIS773 4.3 30.0 1.0
CG B:HIS773 4.3 28.4 1.0
CG2 B:THR805 4.4 21.4 1.0
CD1 B:LEU809 4.4 20.9 1.0
CB B:THR805 4.6 21.9 1.0
C15 B:DY11000 4.8 24.4 1.0
N B:LEU770 4.8 24.7 1.0
C10 B:DY11000 5.0 25.9 1.0
CG B:LEU809 5.0 21.1 1.0

Fluorine binding site 7 out of 8 in 6blf

Go back to Fluorine Binding Sites List in 6blf
Fluorine binding site 7 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:33.6
occ:1.00
 F1 B:DY11000 0.0 33.6 1.0
C16 B:DY11000 1.3 33.4 1.0
F2 B:DY11000 2.1 38.6 1.0
F B:DY11000 2.1 31.7 1.0
C13 B:DY11000 2.3 27.1 1.0
C14 B:DY11000 3.1 24.4 1.0
CG2 B:THR805 3.3 21.4 1.0
CB B:THR805 3.3 21.9 1.0
C12 B:DY11000 3.3 24.9 1.0
CA B:THR805 3.8 18.5 1.0
CG B:LEU809 4.0 21.1 1.0
O B:THR805 4.1 19.0 1.0
CD1 B:LEU809 4.1 20.9 1.0
CD2 B:LEU809 4.2 21.1 1.0
C15 B:DY11000 4.3 24.4 1.0
CD1 B:ILE870 4.3 23.6 1.0
C B:THR805 4.4 19.9 1.0
CB B:ASP808 4.5 16.7 1.0
C11 B:DY11000 4.5 25.0 1.0
OG1 B:THR805 4.5 24.2 1.0
OD2 B:ASP808 4.5 28.2 1.0
O B:THR768 4.6 23.1 1.0
CG B:ASP808 4.9 21.2 1.0
C10 B:DY11000 4.9 25.9 1.0

Fluorine binding site 8 out of 8 in 6blf

Go back to Fluorine Binding Sites List in 6blf
Fluorine binding site 8 out of 8 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:31.7
occ:1.00
 F B:DY11000 0.0 31.7 1.0
C16 B:DY11000 1.3 33.4 1.0
F2 B:DY11000 2.1 38.6 1.0
F1 B:DY11000 2.1 33.6 1.0
C13 B:DY11000 2.4 27.1 1.0
C14 B:DY11000 2.9 24.4 1.0
O B:THR768 3.2 23.1 1.0
C12 B:DY11000 3.5 24.9 1.0
N B:LEU770 3.6 24.7 1.0
CA B:LEU770 3.6 25.8 1.0
C B:THR768 3.6 23.9 1.0
CG2 B:THR805 3.8 21.4 1.0
C B:ASP769 3.8 25.0 1.0
O B:ASP769 4.0 24.1 1.0
O B:ALA767 4.1 26.6 1.0
CA B:THR768 4.1 20.8 1.0
CB B:LEU770 4.2 26.8 1.0
C15 B:DY11000 4.2 24.4 1.0
CB B:HIS773 4.3 25.3 1.0
N B:ASP769 4.3 19.2 1.0
O B:HOH1128 4.3 31.1 1.0
CD1 B:LEU770 4.4 32.2 1.0
CB B:THR805 4.6 21.9 1.0
CA B:ASP769 4.6 19.8 1.0
C11 B:DY11000 4.7 25.0 1.0
C B:LEU770 4.8 29.9 1.0
CG B:LEU770 5.0 31.6 1.0
CG B:HIS773 5.0 28.4 1.0
C10 B:DY11000 5.0 25.9 1.0

Reference:

H.P.Su, H.P.Su. N/A N/A.
Page generated: Thu Aug 1 18:12:58 2024

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