Fluorine in PDB 6yjm: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm was solved by A.Goepfert, P.Leonard, N.Triballeau, D.Fleury, P.Mollat, M.Lamers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.47 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.32, 80.24, 51.05, 90, 90.2, 90
R / Rfree (%) 21.3 / 25.6

Other elements in 6yjm:

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 (pdb code 6yjm). 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 the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6yjm

Go back to Fluorine Binding Sites List in 6yjm
Fluorine binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F505

b:14.5
occ:1.00
F28 A:OU5505 0.0 14.5 1.0
C26 A:OU5505 1.3 17.1 1.0
C25 A:OU5505 2.4 14.5 1.0
C27 A:OU5505 2.4 13.6 1.0
O A:ARG437 3.2 13.2 1.0
CG2 A:THR444 3.4 21.6 1.0
CD1 A:ILE446 3.5 22.9 1.0
O A:LEU438 3.6 12.5 1.0
C24 A:OU5505 3.6 14.1 1.0
C22 A:OU5505 3.6 15.5 1.0
CB A:SER440 3.9 17.8 1.0
O A:ILE442 3.9 16.3 1.0
C A:LEU438 4.0 14.3 1.0
CA A:LEU438 4.1 17.3 1.0
C23 A:OU5505 4.1 11.3 1.0
O A:THR444 4.2 31.3 1.0
C A:ARG437 4.2 16.2 1.0
N A:SER440 4.3 14.3 1.0
O A:SER440 4.3 22.5 1.0
N A:THR444 4.4 24.1 1.0
CG1 A:ILE446 4.5 24.3 1.0
CA A:SER440 4.5 15.7 1.0
OG A:SER440 4.6 20.4 1.0
N A:LEU438 4.7 15.6 1.0
CB A:THR444 4.7 25.4 1.0
F29 A:OU5505 4.7 18.1 1.0
N18 A:OU5505 4.8 15.9 1.0
C A:SER440 4.8 19.7 1.0
C A:THR444 4.9 29.6 1.0
CA A:THR444 4.9 26.2 1.0
N A:MET439 4.9 9.3 1.0

Fluorine binding site 2 out of 4 in 6yjm

Go back to Fluorine Binding Sites List in 6yjm
Fluorine binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F505

b:18.1
occ:1.00
F29 A:OU5505 0.0 18.1 1.0
C24 A:OU5505 1.3 14.1 1.0
C25 A:OU5505 2.4 14.5 1.0
C23 A:OU5505 2.4 11.3 1.0
CB A:PHE406 3.2 10.2 1.0
CB A:HIS403 3.3 15.2 1.0
ND1 A:HIS403 3.3 17.2 1.0
CG A:HIS403 3.5 20.5 1.0
C26 A:OU5505 3.6 17.1 1.0
C22 A:OU5505 3.6 15.5 1.0
CD2 A:PHE406 3.7 27.8 1.0
CD2 A:LEU443 3.8 17.6 1.0
CG A:PHE406 3.9 18.1 1.0
O A:HIS403 4.0 15.4 1.0
CA A:HIS403 4.1 14.8 1.0
C27 A:OU5505 4.1 13.6 1.0
CE1 A:HIS403 4.3 20.7 1.0
OG1 A:THR407 4.4 17.4 1.0
CA A:PHE406 4.4 11.0 1.0
N A:THR407 4.5 12.8 1.0
C A:HIS403 4.5 13.3 1.0
C A:PHE406 4.5 17.2 1.0
CD2 A:HIS403 4.6 18.5 1.0
F28 A:OU5505 4.7 14.5 1.0
N18 A:OU5505 4.8 15.9 1.0
C17 A:OU5505 4.9 16.4 1.0
CE2 A:PHE406 4.9 24.6 1.0
NE2 A:HIS403 5.0 16.4 1.0

Fluorine binding site 3 out of 4 in 6yjm

Go back to Fluorine Binding Sites List in 6yjm
Fluorine binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:18.3
occ:1.00
F28 B:OU5505 0.0 18.3 1.0
C26 B:OU5505 1.3 18.9 1.0
C27 B:OU5505 2.4 18.5 1.0
C25 B:OU5505 2.4 18.1 1.0
O B:ARG437 3.3 17.7 1.0
CG2 B:THR444 3.4 23.8 1.0
CD1 B:ILE446 3.5 24.2 1.0
C24 B:OU5505 3.6 20.9 1.0
C22 B:OU5505 3.6 16.0 1.0
O B:LEU438 3.7 17.1 1.0
O B:ILE442 3.8 19.2 1.0
CB B:SER440 3.9 16.3 1.0
O B:THR444 4.0 33.9 1.0
C B:LEU438 4.1 18.5 1.0
C23 B:OU5505 4.1 18.3 1.0
CA B:LEU438 4.1 19.5 1.0
N B:THR444 4.2 23.5 1.0
O B:SER440 4.3 18.6 1.0
C B:ARG437 4.3 22.5 1.0
N B:SER440 4.4 17.7 1.0
CG1 B:ILE446 4.4 26.6 1.0
OG B:SER440 4.5 22.0 1.0
CA B:SER440 4.6 17.0 1.0
CB B:THR444 4.7 22.7 1.0
N B:LEU438 4.7 14.2 1.0
F29 B:OU5505 4.7 14.3 1.0
C B:THR444 4.8 23.7 1.0
N18 B:OU5505 4.8 16.0 1.0
CA B:THR444 4.8 21.7 1.0
C B:SER440 4.8 19.9 1.0
CA B:LEU443 4.9 19.4 1.0
C B:ILE442 4.9 20.0 1.0
C B:LEU443 4.9 18.3 1.0

Fluorine binding site 4 out of 4 in 6yjm

Go back to Fluorine Binding Sites List in 6yjm
Fluorine binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:14.3
occ:1.00
F29 B:OU5505 0.0 14.3 1.0
C24 B:OU5505 1.3 20.9 1.0
C23 B:OU5505 2.4 18.3 1.0
C25 B:OU5505 2.4 18.1 1.0
CB B:PHE406 3.1 18.3 1.0
CB B:HIS403 3.3 16.0 1.0
CD2 B:PHE406 3.5 29.3 1.0
CD2 B:HIS403 3.5 20.2 1.0
CG B:HIS403 3.5 21.2 1.0
C26 B:OU5505 3.6 18.9 1.0
C22 B:OU5505 3.6 16.0 1.0
CD2 B:LEU443 3.7 22.0 1.0
CG B:PHE406 3.7 22.3 1.0
O B:HIS403 4.0 19.0 1.0
CA B:HIS403 4.1 18.7 1.0
C27 B:OU5505 4.1 18.5 1.0
CA B:PHE406 4.4 15.6 1.0
OG1 B:THR407 4.4 12.6 1.0
N B:THR407 4.5 13.3 1.0
C B:PHE406 4.5 15.1 1.0
NE2 B:HIS403 4.5 20.5 1.0
C B:HIS403 4.6 17.3 1.0
ND1 B:HIS403 4.6 22.1 1.0
CE2 B:PHE406 4.7 37.3 1.0
F28 B:OU5505 4.7 18.3 1.0
N18 B:OU5505 4.8 16.0 1.0
C17 B:OU5505 4.8 12.8 1.0
CD1 B:LEU379 4.9 13.0 1.0

Reference:

P.Leonard, N.Triballeau, P.Mollat. Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 To Be Published.
Page generated: Sat Apr 17 15:34:23 2021

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