Fluorine in PDB 9d9y: Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir

All present enzymatic activity of Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir:
3.4.22.66;

The structure of Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir, PDB code: 9d9y was solved by B.Zhao, S.H.Pham, N.Neetu, B.Sankaran, B.V.V.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.98 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	118.464, 118.464, 66.571, 90, 90, 90
R / Rfree (%)	17.5 / 19.8

The binding sites of Fluorine atom in the Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir (pdb code 9d9y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir, PDB code: 9d9y:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:34.6 occ:1.00 F1 A:AG7201 0.0 34.6 1.0 C09 A:AG7201 1.4 33.1 1.0 C08 A:AG7201 2.4 26.8 1.0 C10 A:AG7201 2.4 30.4 1.0 HB2 A:ARG112 2.4 39.6 1.0 H31 A:AG7201 2.5 32.1 1.0 H33 A:AG7201 2.6 36.5 1.0 HG23 A:VAL114 2.6 34.6 1.0 HG22 A:VAL114 2.7 34.6 1.0 CG2 A:VAL114 2.9 28.9 1.0 HG21 A:VAL114 2.9 34.6 1.0 HB A:ILE109 3.0 40.0 1.0 CB A:ARG112 3.2 33.0 1.0 HB3 A:ARG112 3.3 39.6 1.0 O A:ILE109 3.4 29.1 1.0 C07 A:AG7201 3.6 24.9 1.0 C11 A:AG7201 3.6 29.3 1.0 HE1 A:HIS30 3.7 56.3 1.0 HG3 A:ARG112 3.7 54.3 1.0 HG22 A:ILE109 3.8 43.6 1.0 CB A:ILE109 3.9 33.4 1.0 O A:ARG112 3.9 29.1 1.0 H A:ILE109 4.0 27.9 1.0 CG A:ARG112 4.1 45.3 1.0 HB2 A:GLU54 4.1 28.6 1.0 C06 A:AG7201 4.1 30.9 1.0 OE1 A:GLU54 4.2 25.2 1.0 C A:ARG112 4.2 31.6 1.0 H A:ARG112 4.2 33.8 1.0 CG2 A:ILE109 4.2 36.4 1.0 CA A:ARG112 4.2 28.6 1.0 C A:ILE109 4.3 35.8 1.0 HG21 A:ILE109 4.3 43.6 1.0 HG2 A:GLU54 4.3 35.1 1.0 H30 A:AG7201 4.3 29.9 1.0 CB A:VAL114 4.4 24.6 1.0 H34 A:AG7201 4.4 35.2 1.0 CA A:ILE109 4.5 30.0 1.0 CE1 A:HIS30 4.5 46.9 1.0 HD12 A:ILE109 4.5 40.5 1.0 CD A:GLU54 4.6 38.9 1.0 HH11 A:ARG112 4.6 70.5 1.0 N A:ILE109 4.7 23.3 1.0 N A:ARG112 4.7 28.2 1.0 HG2 A:ARG112 4.7 54.3 1.0 O A:LEU113 4.7 33.1 1.0 HB A:VAL114 4.8 29.5 1.0 C A:LEU113 4.8 33.5 1.0 CG A:GLU54 4.8 29.3 1.0 N A:VAL114 4.8 23.4 1.0 HB2 A:GLN110 4.8 42.2 1.0 HD2 A:ARG112 4.8 77.2 1.0 CB A:GLU54 4.9 23.8 1.0 HA A:VAL114 4.9 22.2 1.0 N A:LEU113 4.9 35.9 1.0 ND1 A:HIS30 5.0 47.9 1.0 CA A:VAL114 5.0 18.5 1.0 CG1 A:ILE109 5.0 33.3 1.0

Fluorine binding site 2 out of 2 in the Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Norovirus Gi.1 Norwalk Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:24.0 occ:1.00 F1 B:AG7201 0.0 24.0 1.0 C09 B:AG7201 1.4 19.7 1.0 C10 B:AG7201 2.3 21.0 1.0 C08 B:AG7201 2.4 20.1 1.0 H33 B:AG7201 2.5 25.2 1.0 HB2 B:ARG112 2.5 26.0 1.0 H31 B:AG7201 2.5 24.1 1.0 HG22 B:VAL114 2.7 35.1 1.0 HG23 B:VAL114 2.7 35.1 1.0 HD2 B:ARG112 2.8 29.2 1.0 HG21 B:VAL114 2.9 35.1 1.0 CG2 B:VAL114 2.9 29.3 1.0 HB B:ILE109 3.1 29.1 1.0 O B:ILE109 3.4 20.1 1.0 CB B:ARG112 3.4 21.7 1.0 CD B:ARG112 3.6 24.3 1.0 C11 B:AG7201 3.6 21.1 1.0 C07 B:AG7201 3.6 18.7 1.0 HB3 B:ARG112 3.7 26.0 1.0 HD3 B:ARG112 3.8 29.2 1.0 HE1 B:HIS30 3.8 34.5 1.0 HG23 B:ILE109 3.9 30.0 1.0 O B:HOH308 3.9 34.8 1.0 CB B:ILE109 4.0 24.2 1.0 CG B:ARG112 4.0 22.4 1.0 HB2 B:GLU54 4.1 24.9 1.0 C06 B:AG7201 4.1 18.4 1.0 OE1 B:GLU54 4.1 23.5 1.0 HG3 B:ARG112 4.2 26.9 1.0 O B:ARG112 4.2 23.2 1.0 H B:ARG112 4.3 24.8 1.0 C B:ILE109 4.3 24.0 1.0 H B:ILE109 4.3 23.9 1.0 CG2 B:ILE109 4.3 25.0 1.0 H34 B:AG7201 4.4 25.2 1.0 H30 B:AG7201 4.4 22.4 1.0 HG22 B:ILE109 4.4 30.0 1.0 CB B:VAL114 4.4 23.6 1.0 CE1 B:HIS30 4.4 28.8 1.0 HD12 B:ILE109 4.5 37.2 1.0 CA B:ARG112 4.5 20.8 1.0 C B:ARG112 4.6 22.3 1.0 CA B:ILE109 4.6 19.7 1.0 HB2 B:GLN110 4.7 26.1 1.0 HB B:VAL114 4.7 28.3 1.0 HG2 B:GLU54 4.7 23.7 1.0 CD B:GLU54 4.8 21.7 1.0 NE B:ARG112 4.8 27.0 1.0 HG11 B:VAL114 4.8 36.3 1.0 N B:ARG112 4.8 20.7 1.0 N B:ILE109 4.9 19.9 1.0 HG2 B:ARG112 4.9 26.9 1.0 HE B:ARG112 4.9 32.4 1.0 CB B:GLU54 5.0 20.7 1.0 HD1 B:HIS30 5.0 30.0 1.0

S.Pham, B.Zhao, N.Neetu, B.Sankaran, K.Patil, S.Ramani, Y.Song, M.K.Estes, T.Palzkill, B.V.V.Prasad. Conformational Flexibility Is A Critical Factor in Designing Broad-Spectrum Human Norovirus Protease Inhibitors. J.Virol. 75724 2025.
ISSN: ESSN 1098-5514
PubMed: 39873493
DOI: 10.1128/JVI.01757-24