Atomistry » Fluorine » PDB 5aik-5avy » 5aix
Atomistry »
  Fluorine »
    PDB 5aik-5avy »
      5aix »

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

Go back to Fluorine Binding Sites List in 5aix
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

Go back to Fluorine Binding Sites List in 5aix
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

Go back to Fluorine Binding Sites List in 5aix
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

Go back to Fluorine Binding Sites List in 5aix
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy