Chlorine in PDB 6cdj: Hiv-1 Wild Type Protease with Grl-03314A, 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

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-03314A, 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: 6cdj 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 / 1.13
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.959, 86.077, 46.157, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 17.3

Other elements in 6cdj:

The structure of Hiv-1 Wild Type Protease with Grl-03314A, 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-03314A, 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 6cdj). 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-03314A, 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: 6cdj:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6cdj

Go back to Chlorine Binding Sites List in 6cdj
Chlorine binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-03314A, 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-03314A, 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:Cl203

b:17.9
occ:1.00
O A:HOH391 2.9 26.1 0.5
N A:THR74 3.2 12.6 1.0
ND2 A:ASN88 3.3 12.3 1.0
CA A:GLY73 3.8 13.2 1.0
CB A:ASN88 3.8 11.3 1.0
OG1 A:THR74 3.8 15.5 1.0
CB A:THR74 3.9 13.0 1.0
C A:GLY73 4.0 12.3 1.0
CG A:ASN88 4.1 11.6 1.0
CA A:THR74 4.1 12.2 1.0
O A:HOH341 4.3 20.6 1.0
O A:ASN88 4.7 12.3 1.0
O A:HOH348 4.7 35.8 0.6
O A:THR74 4.8 12.2 1.0
CA A:ASN88 4.9 10.9 1.0
C A:THR74 5.0 11.8 1.0

Chlorine binding site 2 out of 3 in 6cdj

Go back to Chlorine Binding Sites List in 6cdj
Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-03314A, 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-03314A, 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:Cl101

b:15.2
occ:0.75
O B:HOH303 3.1 33.2 1.0
O A:HOH345 3.3 14.6 1.0
NE1 B:TRP6 3.3 13.6 1.0
CZ2 B:TRP6 3.9 14.5 1.0
CE2 B:TRP6 3.9 13.7 1.0
CG2 B:THR4 4.3 19.9 1.0
CD1 B:TRP6 4.5 13.5 1.0
CB B:THR4 4.9 14.8 1.0
O B:HOH284 4.9 30.7 0.5

Chlorine binding site 3 out of 3 in 6cdj

Go back to Chlorine Binding Sites List in 6cdj
Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-03314A, 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 3 of Hiv-1 Wild Type Protease with Grl-03314A, 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:Cl102

b:19.8
occ:1.00
O B:HOH233 2.9 21.3 1.0
O B:HOH296 2.9 35.6 1.0
N B:THR74 3.2 11.8 1.0
ND2 B:ASN88 3.2 11.9 1.0
CA B:GLY73 3.7 12.8 1.0
OG1 B:THR74 3.7 15.0 1.0
CB B:THR74 3.8 12.8 1.0
CB B:ASN88 3.9 11.4 1.0
C B:GLY73 4.0 11.7 1.0
CG B:ASN88 4.0 11.0 1.0
CA B:THR74 4.1 12.0 1.0
O B:HOH239 4.1 16.9 1.0
NE2 B:GLN92 4.3 14.6 1.0
O B:ASN88 4.4 13.8 1.0
O B:HOH246 4.5 34.6 0.5
CD2 B:LEU89 4.6 15.6 1.0
O B:HOH224 4.6 36.3 1.0
O B:THR74 4.7 11.7 1.0
C B:ASN88 4.8 11.3 1.0
CA B:ASN88 4.8 11.4 1.0
C B:THR74 4.9 11.4 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: Sat Dec 12 12:49:23 2020

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