Atomistry » Fluorine » PDB 2rfn-2vfz » 2vd1
Atomistry »
  Fluorine »
    PDB 2rfn-2vfz »
      2vd1 »

Fluorine in PDB 2vd1: Complex Structure of Prostaglandin D2 Synthase at 2.25A.

Enzymatic activity of Complex Structure of Prostaglandin D2 Synthase at 2.25A.

All present enzymatic activity of Complex Structure of Prostaglandin D2 Synthase at 2.25A.:
5.3.99.2;

Protein crystallography data

The structure of Complex Structure of Prostaglandin D2 Synthase at 2.25A., PDB code: 2vd1 was solved by M.Hohwy, L.Spadola, B.Lundquist, K.Von Wachenfeldt, S.Persdotter, P.Hawtin, J.Dahmen, I.Groth-Clausen, R.H.A.Folmer, K.Edman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 123.521, 123.521, 106.289, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 25.5

Other elements in 2vd1:

The structure of Complex Structure of Prostaglandin D2 Synthase at 2.25A. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex Structure of Prostaglandin D2 Synthase at 2.25A. (pdb code 2vd1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Complex Structure of Prostaglandin D2 Synthase at 2.25A., PDB code: 2vd1:

Fluorine binding site 1 out of 1 in 2vd1

Go back to Fluorine Binding Sites List in 2vd1
Fluorine binding site 1 out of 1 in the Complex Structure of Prostaglandin D2 Synthase at 2.25A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex Structure of Prostaglandin D2 Synthase at 2.25A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1200

b:42.5
occ:1.00
F15 B:D281200 0.0 42.5 1.0
C12 B:D281200 1.3 41.4 1.0
C10 B:D281200 2.4 42.5 1.0
C9 B:D281200 2.4 40.0 1.0
OH B:TYR152 2.4 12.8 1.0
C13 B:D281200 2.8 39.9 1.0
OD1 B:ASP96 3.1 12.7 1.0
CB B:MET99 3.2 17.7 1.0
CZ B:TYR152 3.4 15.4 1.0
CG B:MET99 3.5 17.2 1.0
C5 B:D281200 3.6 41.2 1.0
C6 B:D281200 3.6 42.1 1.0
NH1 B:ARG14 4.0 13.6 1.0
NH2 B:ARG14 4.0 20.4 1.0
CZ B:ARG14 4.0 17.8 1.0
C2 B:D281200 4.1 42.8 1.0
SG B:CYS156 4.1 10.6 1.0
CE1 B:TYR152 4.2 16.9 1.0
CE2 B:TYR152 4.2 15.6 1.0
CG B:ASP96 4.3 13.4 1.0
O B:HOH2045 4.3 10.8 1.0
CA B:ASP96 4.6 12.8 1.0
CA B:MET99 4.6 18.4 1.0
NE B:ARG14 4.7 18.8 1.0
CG B:ARG14 4.8 14.2 1.0
CB B:ASP96 4.9 12.6 1.0
O B:ASP96 5.0 13.7 1.0

Reference:

M.Hohwy, L.Spadola, B.Lundquist, P.Hawtin, J.Dahmen, I.Groth-Clausen, E.Nilsson, S.Persdotter, K.Von Wachenfeldt, R.H.A.Folmer, K.Edman. Novel Prostaglandin D Synthase Inhibitors Generated By Fragment-Based Drug Design. J.Med.Chem. V. 51 2178 2008.
ISSN: ISSN 0022-2623
PubMed: 18341273
DOI: 10.1021/JM701509K
Page generated: Mon Jul 14 14:27:40 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy