Bromine in PDB 3g0g: Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3

All present enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3:
3.4.14.5;

The structure of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3, PDB code: 3g0g was solved by Z.Zhang, M.B.Wallace, J.Feng, J.A.Stafford, S.W.Kaldor, L.Shi, R.J.Skene, K.Aertgeerts, B.Lee, A.Jennings, R.Xu, D.Kassel, D.R.Webb, S.L.Gwaltney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	122.906, 122.921, 145.092, 90.00, 114.77, 90.00
R / Rfree (%)	21 / 26.5

The binding sites of Bromine atom in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3 (pdb code 3g0g). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3, PDB code: 3g0g:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br800 b:42.6 occ:0.40 BR7 A:RUM800 0.0 42.6 0.4 C6 A:RUM800 1.9 42.0 1.0 C1 A:RUM800 2.9 40.6 1.0 O A:HOH2 2.9 19.7 1.0 C5 A:RUM800 2.9 41.1 1.0 O8 A:RUM800 3.0 39.6 1.0 O B:HOH1336 3.0 29.0 1.0 O A:TRP629 3.5 33.6 1.0 CD1 A:TYR547 3.7 37.3 1.0 CB A:SER630 3.8 35.2 1.0 O B:HOH921 3.9 43.8 1.0 CG A:TYR547 3.9 37.4 1.0 CE1 A:TYR547 4.0 36.7 1.0 N4 A:RUM800 4.2 41.5 1.0 OG A:SER630 4.2 36.6 1.0 N2 A:RUM800 4.2 41.2 1.0 O A:HOH1 4.3 17.9 1.0 CD2 A:TYR547 4.3 37.5 1.0 C A:TRP629 4.3 32.0 1.0 CZ A:TYR547 4.4 37.3 1.0 CB A:TYR547 4.4 37.2 1.0 CE2 A:TYR547 4.6 34.1 1.0 N A:GLY632 4.6 27.7 1.0 C3 A:RUM800 4.7 40.8 1.0 N A:TYR631 4.7 35.0 1.0 CA A:SER630 4.8 34.4 1.0 CA A:TYR547 4.9 35.5 1.0 N A:SER630 4.9 34.7 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br800 b:49.4 occ:0.40 BR7 B:RUM800 0.0 49.4 0.4 C6 B:RUM800 1.9 46.3 1.0 C5 B:RUM800 2.9 46.2 1.0 C1 B:RUM800 2.9 45.8 1.0 O B:HOH1042 3.0 45.2 1.0 O8 B:RUM800 3.1 45.0 1.0 O B:TRP629 3.4 34.1 1.0 CD1 B:TYR547 3.6 33.3 1.0 OG B:SER630 3.8 35.8 1.0 CE1 B:TYR547 3.8 33.7 1.0 O B:HOH1041 3.8 41.4 1.0 CB B:SER630 3.9 35.6 1.0 CG B:TYR547 3.9 33.8 1.0 N4 B:RUM800 4.1 46.6 1.0 CZ B:TYR547 4.2 33.3 1.0 N2 B:RUM800 4.2 46.8 1.0 CD2 B:TYR547 4.2 33.9 1.0 O B:HOH1038 4.3 42.7 1.0 C B:TRP629 4.4 33.7 1.0 CE2 B:TYR547 4.4 32.8 1.0 CB B:TYR547 4.5 34.0 1.0 N B:TYR631 4.6 37.3 1.0 C3 B:RUM800 4.7 46.2 1.0 N B:GLY632 4.8 37.9 1.0 CA B:SER630 4.9 36.6 1.0 OH B:TYR547 5.0 31.8 1.0 CA B:TYR547 5.0 34.5 1.0 N B:SER630 5.0 34.8 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br800 b:46.4 occ:0.40 BR7 C:RUM800 0.0 46.4 0.4 C6 C:RUM800 1.9 42.2 1.0 O B:HOH1278 2.9 48.7 1.0 C1 C:RUM800 2.9 41.1 1.0 C5 C:RUM800 2.9 42.5 1.0 O8 C:RUM800 3.0 41.3 1.0 O B:HOH1240 3.4 48.4 1.0 O C:TRP629 3.6 37.8 1.0 CB C:SER630 3.6 38.5 1.0 OG C:SER630 3.9 39.0 1.0 CD1 C:TYR547 4.0 32.8 1.0 CG C:TYR547 4.1 34.3 1.0 N4 C:RUM800 4.1 43.2 1.0 CE1 C:TYR547 4.2 30.9 1.0 N2 C:RUM800 4.2 42.7 1.0 CD2 C:TYR547 4.3 33.8 1.0 C C:TRP629 4.3 35.6 1.0 CZ C:TYR547 4.4 32.1 1.0 CE2 C:TYR547 4.5 33.3 1.0 N C:TYR631 4.6 33.5 1.0 C3 C:RUM800 4.7 42.8 1.0 CB C:TYR547 4.7 34.3 1.0 CA C:SER630 4.7 37.5 1.0 CB C:TRP629 4.8 34.5 1.0 O B:HOH1263 4.8 32.0 1.0 N C:SER630 4.9 37.3 1.0 N C:GLY632 4.9 30.5 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinone Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br800 b:50.3 occ:0.40 BR7 D:RUM800 0.0 50.3 0.4 C6 D:RUM800 1.9 47.6 1.0 C5 D:RUM800 2.9 47.8 1.0 C1 D:RUM800 2.9 47.6 1.0 O8 D:RUM800 3.0 47.3 1.0 O B:HOH1120 3.1 39.0 1.0 CB D:SER630 3.6 40.2 1.0 O D:TRP629 3.8 39.1 1.0 OG D:SER630 3.9 41.8 1.0 N4 D:RUM800 4.1 48.3 1.0 CD1 D:TYR547 4.2 37.4 1.0 N2 D:RUM800 4.2 47.6 1.0 CG D:TYR547 4.2 37.6 1.0 CE1 D:TYR547 4.3 38.1 1.0 CD2 D:TYR547 4.3 37.5 1.0 O B:HOH1117 4.3 34.6 1.0 CZ D:TYR547 4.4 38.1 1.0 C D:TRP629 4.4 38.4 1.0 CE2 D:TYR547 4.4 38.3 1.0 N D:TYR631 4.5 38.4 1.0 O B:HOH1156 4.6 33.8 1.0 CA D:SER630 4.7 38.8 1.0 C3 D:RUM800 4.7 47.9 1.0 N D:SER630 4.9 38.0 1.0 CB D:TYR547 4.9 36.8 1.0 N D:GLY632 4.9 39.7 1.0

Z.Zhang, M.B.Wallace, J.Feng, J.A.Stafford, R.J.Skene, L.Shi, B.Lee, K.Aertgeerts, A.Jennings, R.Xu, D.B.Kassel, S.W.Kaldor, M.Navre, D.R.Webb, S.L.Gwaltney. Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV. J.Med.Chem. V. 54 510 2011.
ISSN: ISSN 0022-2623
PubMed: 21186796
DOI: 10.1021/JM101016W