Fluorine in PDB 9dap: Human Norovirus Gii.3 Protease in Complex with Rupintrivir

The structure of Human Norovirus Gii.3 Protease in Complex with Rupintrivir, PDB code: 9dap was solved by 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)	48.66 / 2.71
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.329, 97.329, 43.77, 90, 90, 120
R / Rfree (%)	18.6 / 24

The binding sites of Fluorine atom in the Human Norovirus Gii.3 Protease in Complex with Rupintrivir (pdb code 9dap). 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 Human Norovirus Gii.3 Protease in Complex with Rupintrivir, PDB code: 9dap:

Fluorine binding site 1 out of 1 in the Human Norovirus Gii.3 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 Gii.3 Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:52.1 occ:1.00 F1 A:AG7201 0.0 52.1 1.0 C09 A:AG7201 1.3 49.1 1.0 C10 A:AG7201 2.3 53.8 1.0 HB2 A:ARG112 2.4 70.9 1.0 C08 A:AG7201 2.4 50.3 1.0 H33 A:AG7201 2.5 69.6 1.0 H31 A:AG7201 2.6 67.8 1.0 HG23 A:VAL114 2.7 69.3 1.0 HG21 A:VAL114 2.8 69.3 1.0 HB3 A:ARG112 2.8 70.9 1.0 HB A:ILE109 2.9 66.8 1.0 CB A:ARG112 3.0 61.8 1.0 O A:ILE109 3.1 51.9 1.0 CG2 A:VAL114 3.1 59.9 1.0 HD2 A:ARG112 3.1 91.8 1.0 HG23 A:ILE109 3.5 74.1 1.0 HG22 A:VAL114 3.6 69.3 1.0 C11 A:AG7201 3.6 56.2 1.0 C07 A:AG7201 3.6 41.6 1.0 HD3 A:ARG112 3.7 91.8 1.0 CD A:ARG112 3.7 79.2 1.0 CB A:ILE109 3.8 49.0 1.0 CG A:ARG112 4.0 75.0 1.0 HG3 A:GLU54 4.0 65.5 1.0 O A:ARG112 4.0 58.2 1.0 HG2 A:GLU54 4.0 65.5 1.0 CG2 A:ILE109 4.0 55.3 1.0 CA A:ARG112 4.1 63.8 1.0 H A:ARG112 4.1 76.6 1.0 C A:ILE109 4.1 49.2 1.0 C A:ARG112 4.1 60.1 1.0 C06 A:AG7201 4.1 46.8 1.0 OE2 A:GLU54 4.1 58.5 1.0 H A:ILE109 4.1 56.4 1.0 HG22 A:ILE109 4.2 74.1 1.0 H34 A:AG7201 4.3 72.4 1.0 CG A:GLU54 4.4 55.6 1.0 HD11 A:ILE109 4.4 77.4 1.0 H30 A:AG7201 4.4 57.2 1.0 CA A:ILE109 4.4 46.0 1.0 HB A:VAL114 4.4 58.3 1.0 CB A:VAL114 4.4 50.8 1.0 HB2 A:GLN110 4.5 65.4 1.0 HE2 A:HIS30 4.5 83.9 1.0 N A:ARG112 4.5 68.7 1.0 HG2 A:ARG112 4.5 86.1 1.0 CD A:GLU54 4.6 58.1 1.0 HG3 A:ARG112 4.6 86.1 1.0 N A:ILE109 4.7 41.5 1.0 HD12 A:ILE109 4.8 77.4 1.0 HA A:ARG112 4.9 72.1 1.0 N A:THR113 4.9 62.8 1.0 HG21 A:ILE109 4.9 74.1 1.0 CD1 A:ILE109 4.9 56.2 1.0 CG1 A:ILE109 4.9 49.0 1.0 O A:THR113 5.0 47.9 1.0 NE2 A:HIS30 5.0 70.7 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