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Chlorine 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:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where 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:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5ult

Go back to Chlorine Binding Sites List in 5ult
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl502

b:23.9
occ:0.75
N A:THR74 3.2 21.8 1.0
ND2 A:ASN88 3.2 21.6 1.0
CA A:GLY73 3.8 23.6 1.0
OG1 A:THR74 3.8 27.6 1.0
CB A:THR74 3.8 25.2 1.0
CB A:ASN88 3.9 20.0 1.0
C A:GLY73 4.0 22.3 1.0
CG A:ASN88 4.1 20.6 1.0
CA A:THR74 4.1 22.6 1.0
O A:HOH628 4.4 32.5 1.0
O A:THR74 4.7 24.1 1.0
O A:ASN88 4.8 23.2 1.0
CA A:ASN88 4.9 19.6 1.0
C A:THR74 4.9 22.2 1.0

Chlorine binding site 2 out of 2 in 5ult

Go back to Chlorine Binding Sites List in 5ult
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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
B:Cl202

b:33.6
occ:1.00
O B:HOH365 3.0 35.7 0.5
NE1 B:TRP6 3.3 22.7 1.0
O A:HOH619 3.3 25.4 1.0
CZ2 B:TRP6 3.9 25.1 1.0
CE2 B:TRP6 3.9 23.6 1.0
CG2 B:THR4 4.4 30.9 1.0
CD1 B:TRP6 4.4 21.6 1.0
CB B:THR4 4.9 25.9 1.0
O A:HOH611 5.0 25.3 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: Sat Jul 12 09:24:42 2025

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