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Chlorine 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
Sodium (Na) 1 atom

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 6cdl

Go back to Chlorine Binding Sites List in 6cdl
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl502

b:15.9
occ:1.00
 O A:HOH674 3.1 36.9 1.0
N A:THR74 3.2 10.3 1.0
ND2 A:ASN88 3.2 9.9 1.0
CA A:GLY73 3.7 10.2 1.0
CB A:ASN88 3.8 9.2 1.0
OG1 A:THR74 3.8 13.7 1.0
CB A:THR74 3.8 11.6 1.0
C A:GLY73 4.0 9.3 1.0
CG A:ASN88 4.0 8.7 1.0
CA A:THR74 4.1 10.2 1.0
O A:HOH645 4.3 20.7 1.0
O A:ASN88 4.6 10.1 1.0
O A:THR74 4.8 10.4 1.0
CA A:ASN88 4.8 8.2 1.0
O A:HOH644 4.9 29.9 0.5
C A:THR74 5.0 8.9 1.0
C A:ASN88 5.0 8.9 1.0

Chlorine binding site 2 out of 2 in 6cdl

Go back to Chlorine Binding Sites List in 6cdl
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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
B:Cl202

b:15.3
occ:1.00
 NE1 B:TRP6 3.3 10.6 1.0
O A:HOH638 3.3 12.4 1.0
CZ2 B:TRP6 3.8 11.3 1.0
CE2 B:TRP6 3.9 10.4 1.0
CG2 B:THR4 4.2 17.2 1.0
CD1 B:TRP6 4.4 10.8 1.0
CB B:THR4 4.8 11.1 1.0
O B:HOH363 4.9 25.5 0.5

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: Sat Jul 12 12:22:02 2025

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