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Sodium in PDB 6cdl: Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand, PDB code: 6cdl 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 / 1.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.260, 85.910, 46.051, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.1

Other elements in 6cdl:

The structure of Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand (pdb code 6cdl). 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-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand, PDB code: 6cdl:

Sodium binding site 1 out of 1 in 6cdl

Go back to Sodium Binding Sites List in 6cdl
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand


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-03214A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:19.9
occ:1.00
O A:ASP60 2.3 12.9 1.0
O A:HOH646 2.3 19.1 1.0
O A:HOH628 2.4 26.1 1.0
O A:HOH614 2.4 20.5 1.0
O A:HOH667 2.4 21.9 1.0
O A:HOH668 2.9 28.7 1.0
C A:ASP60 3.3 11.5 1.0
N A:ASP60 3.7 11.7 1.0
CA A:ASP60 4.0 10.7 1.0
O A:ARG41 4.2 15.6 1.0
CB A:ASP60 4.4 14.7 1.0
CB A:GLN61 4.4 16.1 1.0
N A:GLN61 4.4 12.7 1.0
O A:HOH682 4.5 29.9 0.5
N A:ARG41 4.5 19.1 1.0
O A:GLN61 4.6 15.6 1.0
CD1 A:ILE62 4.7 13.1 1.0
O A:PRO39 4.7 19.1 1.0
C A:TYR59 4.7 9.5 1.0
CA A:GLN61 4.7 12.8 1.0
OE1 A:GLN61 4.7 42.8 1.0
C A:GLN61 4.7 12.9 1.0
CA A:GLY40 4.8 19.2 1.0
CG A:ARG41 4.9 39.5 1.0

Reference:

A.K.Ghosh, P.R Nyalapatla, S.Kovela, K.V.Rao, M.Brindisi, H.L.Osswald, M.Amano, M.Aoki, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Design and Synthesis of Highly Potent Hiv-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems As Novel P2 Ligands: Structure-Activity Studies, Biological and X-Ray Structural Analysis. J. Med. Chem. V. 61 4561 2018.
ISSN: ISSN 1520-4804
PubMed: 29763303
DOI: 10.1021/ACS.JMEDCHEM.8B00298
Page generated: Tue Oct 8 06:34:40 2024

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