Zinc in PDB 2xx9: Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution.

The structure of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution., PDB code: 2xx9 was solved by S.E.Ward, M.Harries, L.Aldegheri, N.E.Austin, S.Ballantine, E.Ballini, D.M.Bradley, B.D.Bax, B.P.Clarke, A.J.Harris, S.A.Harrison, R.A.Melarange, C.Mookherjee, J.Mosley, G.Dalnegro, B.Oliosi, K.J.Smith, K.M.Thewlis, P.M.Woollard, S.P.Yusaf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.49 / 1.97
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.188, 164.152, 47.456, 90.00, 90.00, 90.00
R / Rfree (%)	18.522 / 22.388

The structure of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Zinc atom in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. (pdb code 2xx9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution., PDB code: 2xx9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1264 b:40.5 occ:1.00 OE1 B:GLU166 1.8 34.8 1.0 OE1 A:GLU42 2.0 36.6 1.0 NE2 A:HIS46 2.1 35.4 1.0 O1 A:SO41263 2.2 37.2 1.0 CD B:GLU166 2.6 37.0 1.0 OE2 B:GLU166 2.8 36.3 1.0 CD A:GLU42 2.9 36.0 1.0 CD2 A:HIS46 3.0 35.7 1.0 CE1 A:HIS46 3.1 37.5 1.0 OE2 A:GLU42 3.2 32.8 1.0 S A:SO41263 3.3 43.4 1.0 O4 A:SO41263 3.7 47.8 1.0 O3 A:SO41263 3.8 49.6 1.0 CG B:GLU166 4.0 34.7 1.0 CD2 A:LEU241 4.1 34.9 1.0 CG A:HIS46 4.2 36.7 1.0 ND1 A:HIS46 4.2 34.4 1.0 CG A:GLU42 4.3 32.2 1.0 N B:SER168 4.3 32.6 1.0 O B:ALA165 4.6 33.1 1.0 O2 A:SO41263 4.6 47.1 1.0 CB A:GLU42 4.6 30.6 1.0 CB B:GLU166 4.6 35.6 1.0 CB B:SER168 4.8 32.3 1.0 CA B:SER168 4.8 32.0 1.0 CD2 A:LEU246 4.9 41.0 1.0 CA B:GLU166 4.9 34.6 1.0 CA B:PRO167 5.0 34.3 1.0 C B:PRO167 5.0 33.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1263 b:48.3 occ:1.00 NE2 B:HIS23 1.9 36.3 1.0 OE2 B:GLU30 2.1 43.5 1.0 CD B:GLU30 2.8 42.2 1.0 OE1 B:GLU30 2.8 39.6 1.0 CD2 B:HIS23 2.9 40.9 1.0 CE1 B:HIS23 2.9 39.0 1.0 ND1 B:HIS23 4.0 40.5 1.0 CD B:LYS20 4.0 41.7 1.0 CG B:HIS23 4.0 43.8 1.0 NZ B:LYS20 4.0 42.6 1.0 CD1 B:LEU26 4.2 60.7 1.0 CG B:GLU30 4.3 43.2 1.0 O B:GLU30 4.3 40.5 1.0 CE B:LYS20 4.6 41.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1264 b:35.8 occ:1.00 OE1 B:GLU42 1.9 28.8 1.0 NE2 B:HIS46 2.0 32.9 1.0 O B:HOH2194 2.2 31.0 1.0 CD B:GLU42 2.9 32.0 1.0 CD2 B:HIS46 2.9 34.9 1.0 CE1 B:HIS46 3.0 37.5 1.0 OE2 B:GLU42 3.2 33.5 1.0 CD2 B:LEU241 3.6 32.5 1.0 O B:HOH2029 4.0 44.2 1.0 CE B:LYS45 4.0 35.6 1.0 O B:HOH2010 4.0 55.5 1.0 NZ B:LYS45 4.1 32.5 1.0 ND1 B:HIS46 4.1 37.4 1.0 CG B:HIS46 4.1 35.0 1.0 OE1 B:GLN244 4.2 49.2 1.0 CG B:GLU42 4.3 29.8 1.0 CB B:GLU42 4.6 28.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1263 b:47.0 occ:1.00 O C:HOH2155 1.9 39.2 1.0 OD2 C:ASP65 2.1 36.5 1.0 O C:HOH2156 2.3 49.2 1.0 CG C:ASP65 2.8 39.2 1.0 OD1 C:ASP65 2.8 40.4 1.0 OD2 C:ASP67 4.2 53.2 1.0 CB C:ASP65 4.3 37.6 1.0 CB C:ASP67 4.5 48.1 1.0 O C:HOH2048 4.8 43.3 1.0 CG2 C:THR68 4.9 46.2 1.0 CG C:ASP67 4.9 50.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 1-((2-Fluoro-4-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Phenyl)Methyl)-2-Pyrrolidinone in Complex with the Ligand Binding Domain of the Rat GLUA2 Receptor and Glutamate at 2.2A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1264 b:74.2 occ:1.00 OE1 C:GLU42 2.2 48.2 1.0 NE2 C:HIS46 2.3 59.7 1.0 O C:HOH2157 2.5 65.9 1.0 O C:HOH2145 2.9 70.6 1.0 CD2 C:HIS46 3.0 58.6 1.0 CD C:GLU42 3.2 47.8 1.0 CE1 C:HIS46 3.5 60.7 1.0 NZ C:LYS45 3.5 63.6 1.0 OE2 C:GLU42 3.6 51.4 1.0 CE C:LYS45 3.6 62.1 1.0 CD2 C:LEU241 3.8 38.9 1.0 OE1 C:GLN244 4.1 55.0 1.0 CD1 C:LEU246 4.2 47.9 1.0 CG C:HIS46 4.3 58.6 1.0 ND1 C:HIS46 4.5 60.2 1.0 CG C:GLU42 4.5 44.7 1.0 CB C:GLU42 4.8 42.3 1.0 O C:GLU42 5.0 43.1 1.0 CD C:GLN244 5.0 51.2 1.0 NE2 C:GLN244 5.0 52.9 1.0

S.E.Ward, M.Harries, L.Aldegheri, N.E.Austin, S.Ballantine, E.Ballini, D.M.Bradley, B.D.Bax, B.P.Clarke, A.J.Harris, S.A.Harrison, R.A.Melarange, C.Mookherjee, J.Mosley, G.Dal Negro, B.Oliosi, K.J.Smith, K.M.Thewlis, P.M.Woollard, S.P.Yusaf. Integration of Lead Optimization with Crystallography For A Membrane-Bound Ion Channel Target: Discovery of A New Class of Ampa Receptor Positive Allosteric Modulators. J.Med.Chem. V. 54 78 2011.
ISSN: ISSN 0022-2623
PubMed: 21128618
DOI: 10.1021/JM100679E