Chlorine in PDB 5upz: Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group, PDB code: 5upz 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 / 1.27
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.175, 86.418, 45.828, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 19.8

Other elements in 5upz:

The structure of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group (pdb code 5upz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group, PDB code: 5upz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5upz

Go back to Chlorine Binding Sites List in 5upz
Chlorine binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:12.4
occ:0.80
O A:HOH417 2.9 31.1 0.5
O A:HOH324 3.0 24.9 1.0
N A:THR74 3.2 10.6 1.0
ND2 A:ASN88 3.2 9.9 1.0
CA A:GLY73 3.7 10.7 1.0
CB A:ASN88 3.8 8.4 1.0
OG1 A:THR74 3.8 13.5 1.0
CB A:THR74 3.9 12.4 1.0
C A:GLY73 4.0 10.1 1.0
CG A:ASN88 4.0 9.1 1.0
CA A:THR74 4.2 11.2 1.0
O A:HOH344 4.3 21.5 1.0
O A:HOH363 4.3 25.8 0.5
O A:ASN88 4.7 10.0 1.0
OD1 A:ASP30 4.8 24.9 1.0
O A:THR74 4.8 11.0 1.0
CA A:ASN88 4.9 8.4 1.0

Chlorine binding site 2 out of 3 in 5upz

Go back to Chlorine Binding Sites List in 5upz
Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:14.3
occ:0.80
O B:HOH326 3.2 24.8 1.0
O A:HOH356 3.2 12.6 1.0
NE1 B:TRP6 3.3 11.2 1.0
CZ2 B:TRP6 3.9 10.9 1.0
CE2 B:TRP6 3.9 10.5 1.0
CG2 B:THR4 4.3 16.4 1.0
CD1 B:TRP6 4.5 10.6 1.0
CB B:THR4 4.9 11.4 1.0
O B:HOH250 4.9 19.3 0.5

Chlorine binding site 3 out of 3 in 5upz

Go back to Chlorine Binding Sites List in 5upz
Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:15.4
occ:0.80
O B:HOH231 2.9 17.3 1.0
ND2 B:ASN88 3.1 10.5 1.0
N B:THR74 3.1 9.0 1.0
O B:HOH321 3.2 28.4 1.0
OG1 B:THR74 3.7 13.0 1.0
CA B:GLY73 3.8 10.3 1.0
CB B:THR74 3.8 10.1 1.0
CB B:ASN88 3.8 9.9 1.0
C B:GLY73 4.0 9.2 1.0
CG B:ASN88 4.0 9.0 1.0
O B:HOH245 4.1 13.8 1.0
CA B:THR74 4.1 9.3 1.0
NE2 B:GLN92 4.4 10.9 1.0
O B:ASN88 4.5 11.4 1.0
CD2 B:LEU89 4.6 13.5 1.0
O B:THR74 4.7 9.9 1.0
C B:ASN88 4.8 9.9 1.0
CA B:ASN88 4.8 8.9 1.0
O B:HOH220 4.9 28.5 1.0
C B:THR74 5.0 9.0 1.0

Reference:

A.K.Ghosh, M.Brindisi, P.R.Nyalapatla, J.Takayama, J.R.Ella-Menye, S.Yashchuk, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Design of Novel Hiv-1 Protease Inhibitors Incorporating Isophthalamide-Derived P2-P3 Ligands: Synthesis, Biological Evaluation and X-Ray Structural Studies of Inhibitor-Hiv-1 Protease Complex. Bioorg. Med. Chem. V. 25 5114 2017.
ISSN: ESSN 1464-3391
PubMed: 28434781
DOI: 10.1016/J.BMC.2017.04.005
Page generated: Sat Dec 12 12:31:51 2020

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