Manganese in PDB 6nem: 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease

The structure of 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 6nem was solved by J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.15 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.505, 100.996, 66.204, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.3

The binding sites of Manganese atom in the 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease (pdb code 6nem). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 6nem:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:31.2 occ:1.00 H011 A:KKS304 2.0 34.4 1.0 OE2 A:GLU119 2.1 33.9 1.0 O01 A:KKS304 2.2 28.7 1.0 OD2 A:ASP108 2.2 27.2 1.0 O A:ILE120 2.2 30.7 1.0 NE2 A:HIS41 2.3 25.6 1.0 O30 A:KKS304 2.3 30.7 1.0 C29 A:KKS304 2.9 30.9 1.0 C02 A:KKS304 3.0 28.4 1.0 CG A:ASP108 3.0 26.0 1.0 CD A:GLU119 3.1 33.3 1.0 CE1 A:HIS41 3.1 27.2 1.0 OD1 A:ASP108 3.2 22.8 1.0 CD2 A:HIS41 3.3 25.3 1.0 HE1 A:HIS41 3.3 32.6 1.0 H A:ILE120 3.3 29.5 1.0 C A:ILE120 3.4 29.3 1.0 HD2 A:HIS41 3.5 30.4 1.0 HZ1 A:LYS134 3.6 54.5 1.0 HB A:ILE120 3.6 34.3 1.0 MN A:MN302 3.7 49.6 1.0 OE1 A:GLU119 3.7 33.8 1.0 HZ2 A:LYS134 3.8 54.5 1.0 N A:ILE120 3.8 24.6 1.0 O A:HOH420 3.8 30.7 1.0 HE3 A:LYS134 3.9 53.5 1.0 O A:HOH480 4.0 44.2 1.0 CA A:ILE120 4.0 27.8 1.0 NZ A:LYS134 4.0 45.4 1.0 HG3 A:GLU119 4.0 39.0 1.0 HA2 A:GLY121 4.0 36.8 1.0 N28 A:KKS304 4.2 32.2 1.0 CG A:GLU119 4.2 32.5 1.0 ND1 A:HIS41 4.2 26.9 1.0 C03 A:KKS304 4.3 30.0 1.0 CB A:ILE120 4.3 28.6 1.0 CG A:HIS41 4.3 26.8 1.0 CB A:ASP108 4.4 23.1 1.0 N A:GLY121 4.5 29.7 1.0 HA A:GLU119 4.5 34.8 1.0 HG22 A:ILE120 4.5 33.2 1.0 CE A:LYS134 4.5 44.6 1.0 H281 A:KKS304 4.6 38.6 1.0 HB2 A:ASP108 4.6 27.7 1.0 C A:GLU119 4.7 28.7 1.0 CA A:GLY121 4.7 30.7 1.0 OE1 A:GLU80 4.7 28.1 1.0 H031 A:KKS304 4.8 36.0 1.0 HB3 A:ASP108 4.8 27.7 1.0 HZ3 A:LYS134 4.8 54.5 1.0 HG2 A:GLU119 4.8 39.0 1.0 HA A:ILE120 4.9 33.4 1.0 CG2 A:ILE120 5.0 27.7 1.0 HD1 A:HIS41 5.0 32.3 1.0 CA A:GLU119 5.0 29.0 1.0

Manganese binding site 2 out of 3 in the 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:49.6 occ:1.00 OE1 A:GLU80 2.0 28.1 1.0 O A:HOH420 2.1 30.7 1.0 OD1 A:ASP108 2.1 22.8 1.0 O01 A:KKS304 2.2 28.7 1.0 O A:HOH481 2.2 31.1 1.0 O A:HOH441 2.2 28.3 1.0 H011 A:KKS304 2.7 34.4 1.0 H031 A:KKS304 3.0 36.0 1.0 HE1 A:HIS41 3.1 32.6 1.0 C02 A:KKS304 3.1 28.4 1.0 CG A:ASP108 3.2 26.0 1.0 CD A:GLU80 3.2 27.4 1.0 C03 A:KKS304 3.4 30.0 1.0 HB2 A:GLU80 3.4 30.3 1.0 MN A:MN301 3.7 31.2 1.0 OD2 A:ASP108 3.7 27.2 1.0 HA A:ASP108 3.8 30.4 1.0 CE1 A:HIS41 3.8 27.2 1.0 HG2 A:GLU80 4.0 31.3 1.0 CG A:GLU80 4.0 26.1 1.0 O A:HOH511 4.0 53.1 1.0 O A:HOH463 4.1 40.7 1.0 OE2 A:GLU80 4.1 29.4 1.0 CB A:GLU80 4.1 25.3 1.0 O A:PRO107 4.2 25.9 1.0 O A:HOH480 4.2 44.2 1.0 O A:HOH442 4.3 39.0 1.0 HA A:GLU80 4.3 30.7 1.0 NE2 A:HIS41 4.3 25.6 1.0 O A:LEU106 4.3 33.1 1.0 OE1 A:GLU119 4.3 33.8 1.0 CB A:ASP108 4.3 23.1 1.0 C29 A:KKS304 4.4 30.9 1.0 CA A:ASP108 4.4 25.3 1.0 OE2 A:GLU119 4.4 33.9 1.0 C A:PRO107 4.4 25.7 1.0 N A:ASP108 4.5 25.3 1.0 HB3 A:ASP108 4.7 27.7 1.0 CA A:GLU80 4.7 25.6 1.0 O30 A:KKS304 4.8 30.7 1.0 CD A:GLU119 4.8 33.3 1.0 C04 A:KKS304 4.8 28.5 1.0 HA A:PRO107 4.9 37.1 1.0 HG3 A:GLU80 4.9 31.3 1.0 ND1 A:HIS41 4.9 26.9 1.0 HB3 A:GLU80 4.9 30.3 1.0 H A:ASP108 5.0 30.3 1.0

Manganese binding site 3 out of 3 in the 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 3-Hydroxy-5-[(Naphthalen-1-Yl)Methyl]-6-[4-(1H-Tetrazol-5-Yl) Phenyl]Pyridin-2(1H)-One Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:64.0 occ:0.42 O A:HOH406 2.1 52.4 1.0 NE2 A:HIS74 2.3 72.3 1.0 O A:HOH513 2.4 0.6 0.5 CD2 A:HIS74 3.3 69.7 1.0 CE1 A:HIS74 3.3 68.7 1.0 HD2 A:HIS74 3.4 83.7 1.0 HE1 A:HIS74 3.5 82.5 1.0 HE1 A:PHE53 3.8 55.3 1.0 HG3 A:PRO68 4.3 83.2 0.0 ND1 A:HIS74 4.4 63.8 1.0 CG A:HIS74 4.4 58.7 1.0 HG2 A:PRO68 4.4 83.2 0.0 CE1 A:PHE53 4.7 46.0 1.0 HZ A:PHE53 4.8 56.6 1.0 CG A:PRO68 4.9 69.3 0.0

H.Y.Sagong, J.D.Bauman, A.Nogales, L.Martinez-Sobrido, E.Arnold, E.J.Lavoie. Aryl and Arylalkyl Substituted 3-Hydroxypyridin-2(1H)-Ones: Synthesis and Evaluation As Inhibitors of Influenza A Endonuclease. Chemmedchem V. 14 1204 2019.
ISSN: ESSN 1860-7187
PubMed: 30983160
DOI: 10.1002/CMDC.201900084