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Sodium in PDB 5ult: Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group)

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group), PDB code: 5ult was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.53
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.336, 86.776, 45.252, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.5

Other elements in 5ult:

The structure of Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group) (pdb code 5ult). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group), PDB code: 5ult:

Sodium binding site 1 out of 1 in 5ult

Go back to Sodium Binding Sites List in 5ult
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Wild Type Protease with Grl-100-13A (A Crown-Like Oxotricyclic Core As the P2-Ligand with the Sulfonamide Isostere As the P2' Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:34.2
occ:1.00
O A:ASP60 2.2 26.1 1.0
O A:HOH617 2.3 36.8 1.0
O A:HOH631 2.3 34.9 1.0
O A:HOH613 2.3 34.8 1.0
O A:HOH634 2.8 30.1 0.5
C A:ASP60 3.3 23.3 1.0
N A:ASP60 3.7 23.1 1.0
CA A:ASP60 4.0 23.6 1.0
O A:ARG41 4.3 33.6 1.0
CD1 A:ILE62 4.3 33.4 1.0
N A:GLN61 4.4 25.6 1.0
CB A:GLN61 4.4 30.2 1.0
CB A:ASP60 4.4 25.8 1.0
O A:GLN61 4.5 31.5 1.0
O A:PRO39 4.6 34.9 1.0
C A:TYR59 4.6 21.5 1.0
N A:ARG41 4.7 35.0 1.0
C A:GLN61 4.7 26.2 1.0
CA A:GLN61 4.7 25.8 1.0
CA A:GLY40 4.8 39.5 1.0

Reference:

A.K.Ghosh, K.V.Rao, P.R.Nyalapatla, H.L.Osswald, C.D.Martyr, M.Aoki, H.Hayashi, J.Agniswamy, Y.F.Wang, H.Bulut, D.Das, I.T.Weber, H.Mitsuya. Design and Development of Highly Potent Hiv-1 Protease Inhibitors with A Crown-Like Oxotricyclic Core As the P2-Ligand to Combat Multidrug-Resistant Hiv Variants. J. Med. Chem. V. 60 4267 2017.
ISSN: ISSN 1520-4804
PubMed: 28418652
DOI: 10.1021/ACS.JMEDCHEM.7B00172
Page generated: Tue Dec 15 11:42:45 2020

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