Atomistry » Sodium » PDB 6e8t-6eqe » 6e9a
Atomistry »
  Sodium »
    PDB 6e8t-6eqe »
      6e9a »

Sodium in PDB 6e9a: Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand, PDB code: 6e9a 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 / 1.22
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.372, 86.276, 46.020, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.8

Other elements in 6e9a:

The structure of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand (pdb code 6e9a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand, PDB code: 6e9a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6e9a

Go back to Sodium Binding Sites List in 6e9a
Sodium binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:19.0
occ:1.00
O A:HOH637 2.3 19.5 1.0
O A:ASP60 2.4 13.6 1.0
O A:HOH613 2.4 19.0 1.0
O A:HOH631 2.4 29.6 1.0
O A:HOH651 2.4 20.3 1.0
O A:HOH655 2.7 28.5 1.0
C A:ASP60 3.4 13.1 1.0
N A:ASP60 3.7 12.3 1.0
CA A:ASP60 4.0 12.4 1.0
O A:ARG41 4.2 15.8 1.0
O A:HOH628 4.3 25.4 0.5
CB A:ASP60 4.3 15.2 1.0
CB A:GLN61 4.4 16.4 1.0
N A:GLN61 4.5 13.0 1.0
N A:ARG41 4.5 20.4 1.0
O A:GLN61 4.6 16.6 1.0
C A:TYR59 4.7 10.5 1.0
O A:PRO39 4.7 19.0 1.0
CD1 A:ILE62 4.8 15.0 1.0
CA A:GLN61 4.8 14.0 1.0
CA A:GLY40 4.8 19.6 1.0
C A:GLN61 4.8 13.9 1.0
OE1 A:GLN61 4.8 40.0 1.0
C A:GLY40 5.0 17.8 1.0

Sodium binding site 2 out of 2 in 6e9a

Go back to Sodium Binding Sites List in 6e9a
Sodium binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:19.8
occ:0.50
O B:HOH324 2.3 23.6 1.0
O B:ASP60 2.5 17.6 1.0
O B:HOH355 2.5 39.3 1.0
O B:HOH383 2.5 33.9 0.5
O B:HOH319 2.6 30.1 1.0
C B:ASP60 3.5 15.8 1.0
N B:ASP60 3.6 14.7 1.0
O B:HOH343 3.6 24.8 0.5
CA B:ASP60 3.9 14.6 1.0
O B:ARG41 4.1 15.8 1.0
CB B:ASP60 4.2 16.5 1.0
C B:TYR59 4.5 11.2 1.0
O B:PRO39 4.6 17.7 1.0
N B:GLN61 4.6 14.2 1.0
CD1 B:ILE62 4.7 18.6 1.0
CB B:GLN61 4.8 17.6 1.0
N B:ARG41 4.8 13.0 1.0
CA B:TYR59 4.9 12.3 1.0
CA B:GLY40 4.9 14.7 1.0
C B:GLN61 5.0 15.9 1.0

Reference:

A.K.Ghosh, J.N.Williams, R.Y.Ho, H.M.Simpson, S.I.Hattori, H.Hayashi, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Design and Synthesis of Potent Hiv-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold As the P2 Ligands: Structure-Activity Studies and Biological and X-Ray Structural Studies. J. Med. Chem. V. 61 9722 2018.
ISSN: ISSN 1520-4804
PubMed: 30354121
DOI: 10.1021/ACS.JMEDCHEM.8B01227
Page generated: Tue Dec 15 12:10:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy