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Fluorine in PDB 5aix: Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.

Enzymatic activity of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.

All present enzymatic activity of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.:
2.5.1.18; 5.3.99.2;

Protein crystallography data

The structure of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor., PDB code: 5aix was solved by F.Edfeldt, J.Evenas, M.Lepisto, A.Ward, J.Petersen, L.Wissler, M.Rohman, U.Sivars, K.Svensson, M.Perry, I.Feierberg, X.Zhou, T.Hansson, F.Narjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.65 / 2.10
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 122.228, 122.228, 106.023, 90.00, 90.00, 90.00
R / Rfree (%) 25.63 / 34.295

Other elements in 5aix:

The structure of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. (pdb code 5aix). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor., PDB code: 5aix:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5aix

Go back to Fluorine Binding Sites List in 5aix
Fluorine binding site 1 out of 6 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1201

b:20.4
occ:1.00
 F26 B:KRX1201 0.0 20.4 1.0
C25 B:KRX1201 1.3 25.8 1.0
F27 B:KRX1201 2.2 28.9 1.0
F28 B:KRX1201 2.2 29.9 1.0
C24 B:KRX1201 2.3 23.7 1.0
OE1 B:GLN36 2.6 39.6 1.0
CD B:GLN36 3.4 38.5 1.0
N21 B:KRX1201 3.5 21.2 1.0
NE2 B:GLN36 4.1 37.8 1.0
CG B:GLN36 4.2 37.0 1.0
C22 B:KRX1201 4.3 22.2 1.0
CD1 B:TRP39 4.5 25.8 1.0
C20 B:KRX1201 4.5 21.4 1.0
NE1 B:TRP39 5.0 23.5 1.0

Fluorine binding site 2 out of 6 in 5aix

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Fluorine binding site 2 out of 6 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1201

b:28.9
occ:1.00
 F27 B:KRX1201 0.0 28.9 1.0
C25 B:KRX1201 1.4 25.8 1.0
F26 B:KRX1201 2.2 20.4 1.0
F28 B:KRX1201 2.2 29.9 1.0
C24 B:KRX1201 2.4 23.7 1.0
CE2 B:PHE9 2.9 25.6 1.0
N21 B:KRX1201 3.1 21.2 1.0
C22 B:KRX1201 3.2 22.2 1.0
OE1 B:GLN36 3.2 39.6 1.0
CZ B:PHE9 3.2 26.0 1.0
CG B:GLN36 3.4 37.0 1.0
CD B:GLN36 3.4 38.5 1.0
CD2 B:PHE9 3.7 24.9 1.0
CD1 B:TRP39 3.9 25.8 1.0
CE1 B:PHE9 4.2 25.1 1.0
C23 B:KRX1201 4.3 21.4 1.0
NE2 B:GLN36 4.4 37.8 1.0
CG B:TRP39 4.5 25.5 1.0
CB B:GLN36 4.5 36.3 1.0
C20 B:KRX1201 4.5 21.4 1.0
NE1 B:TRP39 4.5 23.5 1.0
CA B:GLN36 4.6 36.7 1.0
CG B:PHE9 4.6 24.5 1.0
CB B:TRP39 4.7 28.7 1.0
O B:GLN36 4.8 36.9 1.0
CD1 B:PHE9 4.8 24.5 1.0
CA3 B:GSH1200 4.8 27.8 1.0

Fluorine binding site 3 out of 6 in 5aix

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Fluorine binding site 3 out of 6 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1201

b:29.9
occ:1.00
 F28 B:KRX1201 0.0 29.9 1.0
C25 B:KRX1201 1.4 25.8 1.0
F27 B:KRX1201 2.2 28.9 1.0
F26 B:KRX1201 2.2 20.4 1.0
C24 B:KRX1201 2.4 23.7 1.0
N21 B:KRX1201 2.7 21.2 1.0
CA3 B:GSH1200 3.2 27.8 1.0
C22 B:KRX1201 3.5 22.2 1.0
C20 B:KRX1201 3.9 21.4 1.0
CZ B:PHE9 4.0 26.0 1.0
NE1 B:TRP39 4.1 23.5 1.0
C3 B:GSH1200 4.1 29.5 1.0
CD1 B:TRP39 4.1 25.8 1.0
N3 B:GSH1200 4.2 28.0 1.0
C23 B:KRX1201 4.3 21.4 1.0
CE2 B:PHE9 4.4 25.6 1.0
OE1 B:GLN36 4.5 39.6 1.0
C19 B:KRX1201 4.6 17.8 1.0
O31 B:GSH1200 4.7 31.3 1.0
CE1 B:PHE9 4.7 25.1 1.0
O32 B:GSH1200 4.7 29.3 1.0
CD B:GLN36 5.0 38.5 1.0

Fluorine binding site 4 out of 6 in 5aix

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Fluorine binding site 4 out of 6 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:38.5
occ:1.00
 F26 C:KRX1201 0.0 38.5 1.0
C25 C:KRX1201 1.4 40.3 1.0
F27 C:KRX1201 2.2 39.3 1.0
F28 C:KRX1201 2.2 41.2 1.0
C24 C:KRX1201 2.3 37.2 1.0
NE2 C:GLN36 2.7 35.1 1.0
N21 C:KRX1201 3.6 36.3 1.0
CD C:GLN36 3.8 36.6 1.0
OE1 C:GLN36 4.2 37.3 1.0
C22 C:KRX1201 4.3 34.7 1.0
CD1 C:TRP39 4.4 44.8 1.0
C20 C:KRX1201 4.6 35.1 1.0
NE1 C:TRP39 4.9 43.4 1.0
CB C:GLN36 4.9 36.7 1.0
CG C:GLN36 5.0 36.5 1.0

Fluorine binding site 5 out of 6 in 5aix

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Fluorine binding site 5 out of 6 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:39.3
occ:1.00
 F27 C:KRX1201 0.0 39.3 1.0
C25 C:KRX1201 1.4 40.3 1.0
F26 C:KRX1201 2.2 38.5 1.0
F28 C:KRX1201 2.3 41.2 1.0
C24 C:KRX1201 2.4 37.2 1.0
NE2 C:GLN36 2.7 35.1 1.0
N21 C:KRX1201 2.8 36.3 1.0
CZ C:PHE9 2.9 19.8 1.0
C22 C:KRX1201 3.2 34.7 1.0
CE1 C:PHE9 3.4 20.3 1.0
CE2 C:PHE9 3.8 20.9 1.0
CD1 C:TRP39 3.8 44.8 1.0
CD C:GLN36 3.9 36.6 1.0
NE1 C:TRP39 4.0 43.4 1.0
C20 C:KRX1201 4.2 35.1 1.0
OE1 C:GLN36 4.3 37.3 1.0
C23 C:KRX1201 4.3 33.2 1.0
CA3 C:GSH1200 4.3 24.4 1.0
CD1 C:PHE9 4.5 19.1 1.0
CG C:TRP39 4.7 45.0 1.0
CD2 C:PHE9 4.8 15.2 1.0
CE2 C:TRP39 4.9 43.5 1.0
N3 C:GSH1200 5.0 22.3 1.0

Fluorine binding site 6 out of 6 in 5aix

Go back to Fluorine Binding Sites List in 5aix
Fluorine binding site 6 out of 6 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:41.2
occ:1.00
 F28 C:KRX1201 0.0 41.2 1.0
C25 C:KRX1201 1.4 40.3 1.0
F26 C:KRX1201 2.2 38.5 1.0
F27 C:KRX1201 2.3 39.3 1.0
C24 C:KRX1201 2.4 37.2 1.0
N21 C:KRX1201 3.0 36.3 1.0
C20 C:KRX1201 3.9 35.1 1.0
CA3 C:GSH1200 4.2 24.4 1.0
C22 C:KRX1201 4.3 34.7 1.0
O31 C:GSH1200 4.3 25.4 1.0
NE2 C:GLN36 4.4 35.1 1.0
C3 C:GSH1200 4.4 26.5 1.0
NE1 C:TRP39 4.7 43.4 1.0
N3 C:GSH1200 4.8 22.3 1.0
CB C:ALA105 4.8 23.2 1.0
C19 C:KRX1201 4.9 32.6 1.0
CZ C:PHE9 4.9 19.8 1.0
CD1 C:TRP39 4.9 44.8 1.0

Reference:

F.Edfeldt, J.Even, M.Lepisto, A.Ward, J.Petersen, L.Wissler, M.Rohman, U.Sivars, K.Svensson, M.Perry, I.Feierberg, X.H.Zhou, T.Hansson, F.Narjes. Identification of Indole Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase (Hh-Pgds). Bioorg.Med.Chem.Lett. V. 25 2496 2015.
ISSN: ISSN 0960-894X
PubMed: 25978964
DOI: 10.1016/J.BMCL.2015.04.065
Page generated: Thu Aug 1 07:45:47 2024

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