Chlorine in PDB 6vce: Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand, PDB code: 6vce was solved by Y.-F.Wang, D.W.Kneller, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.48 / 1.18
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.904, 86.207, 46.090, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 15.5

Other elements in 6vce:

The structure of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 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-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand (pdb code 6vce). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand, PDB code: 6vce:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6vce

Go back to Chlorine Binding Sites List in 6vce
Chlorine binding site 1 out of 6 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 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-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:13.7
occ:0.80
 N A:THR74 3.2 11.0 1.0
ND2 A:ASN88 3.3 10.7 1.0
CA A:GLY73 3.7 11.3 1.0
OG1 A:THR74 3.8 13.8 1.0
CB A:ASN88 3.8 10.1 1.0
CB A:THR74 3.8 12.2 1.0
C A:GLY73 4.0 10.9 1.0
CG A:ASN88 4.1 9.6 1.0
CA A:THR74 4.1 10.8 1.0
O A:HOH644 4.3 18.3 1.0
O A:ASN88 4.7 10.3 1.0
O A:THR74 4.8 11.1 1.0
CA A:ASN88 4.9 9.3 1.0
C A:THR74 5.0 10.7 1.0

Chlorine binding site 2 out of 6 in 6vce

Go back to Chlorine Binding Sites List in 6vce
Chlorine binding site 2 out of 6 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 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-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:28.8
occ:0.75
 N A:ARG8 3.2 11.2 1.0
CB A:LYS7 3.5 18.6 0.5
CG A:ARG8 3.6 12.8 0.5
CB A:LYS7 3.7 17.5 0.5
CA A:LYS7 3.8 13.4 0.5
CA A:LYS7 3.8 13.1 0.5
CG A:ARG8 3.8 13.9 0.6
CB A:ARG8 3.9 11.4 0.6
CB A:ARG8 3.9 11.7 0.5
CD A:ARG8 4.0 17.8 0.5
C A:LYS7 4.0 11.2 1.0
CA A:ARG8 4.2 11.1 0.6
CA A:ARG8 4.2 11.3 0.5
CG A:LYS7 4.2 23.8 0.5
O A:HOH616 4.3 26.9 1.0
NE A:ARG8 4.4 21.4 0.5
NH2 B:ARG87 4.4 12.0 1.0
CD A:ARG8 4.5 14.7 0.6
CG A:LYS7 4.8 24.3 0.5
CZ A:ARG8 4.9 21.0 0.5
CZ B:ARG87 5.0 11.4 1.0

Chlorine binding site 3 out of 6 in 6vce

Go back to Chlorine Binding Sites List in 6vce
Chlorine binding site 3 out of 6 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 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-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:21.3
occ:0.75
 O A:HOH707 2.8 32.4 1.0
N A:LYS55 3.2 11.2 1.0
O A:HOH628 3.2 31.4 1.0
CA A:ILE54 3.6 11.2 1.0
CB A:ILE54 3.9 11.9 1.0
C A:ILE54 3.9 11.5 1.0
CB A:LYS55 4.0 13.3 1.0
CG A:PRO79 4.1 11.8 1.0
CA A:LYS55 4.1 10.9 1.0
CG2 A:ILE54 4.2 13.3 1.0
O A:LYS55 4.3 11.6 1.0
O A:HOH704 4.6 25.2 0.5
C A:LYS55 4.7 10.6 1.0
O A:PHE53 4.7 14.4 1.0
CD A:PRO79 4.9 11.4 1.0
N A:ILE54 4.9 12.4 1.0

Chlorine binding site 4 out of 6 in 6vce

Go back to Chlorine Binding Sites List in 6vce
Chlorine binding site 4 out of 6 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:13.4
occ:0.80
 O B:HOH409 3.2 28.9 1.0
O A:HOH645 3.3 13.4 1.0
NE1 B:TRP6 3.3 11.4 1.0
CZ2 B:TRP6 3.9 11.6 1.0
CE2 B:TRP6 3.9 11.0 1.0
CG2 B:THR4 4.2 17.4 1.0
CD1 B:TRP6 4.5 11.9 1.0
CB B:THR4 4.9 12.9 1.0
O B:HOH320 5.0 25.6 0.5

Chlorine binding site 5 out of 6 in 6vce

Go back to Chlorine Binding Sites List in 6vce
Chlorine binding site 5 out of 6 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:14.6
occ:0.75
 O B:HOH400 2.9 32.6 1.0
O B:HOH330 3.0 17.6 1.0
N B:THR74 3.2 10.6 1.0
ND2 B:ASN88 3.2 10.5 1.0
OG1 B:THR74 3.7 13.9 1.0
CA B:GLY73 3.7 11.2 1.0
CB B:THR74 3.8 11.5 1.0
CB B:ASN88 3.8 9.8 1.0
C B:GLY73 4.0 11.1 1.0
CG B:ASN88 4.0 9.3 1.0
CA B:THR74 4.1 10.4 1.0
O B:HOH348 4.1 16.4 1.0
NE2 B:GLN92 4.4 12.8 1.0
O B:HOH345 4.5 28.0 0.5
O B:ASN88 4.5 11.2 1.0
O B:HOH321 4.6 28.6 1.0
CD2 B:LEU89 4.6 13.0 1.0
O B:THR74 4.7 10.8 1.0
C B:ASN88 4.8 9.7 1.0
CA B:ASN88 4.8 9.8 1.0
C B:THR74 4.9 10.3 1.0

Chlorine binding site 6 out of 6 in 6vce

Go back to Chlorine Binding Sites List in 6vce
Chlorine binding site 6 out of 6 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:23.4
occ:0.75
 O1 B:GOL205 2.9 25.2 0.5
O B:HOH311 3.1 22.3 0.5
N B:THR12 3.2 11.3 1.0
C1 B:GOL205 3.6 18.6 0.5
CB B:VAL11 3.7 13.1 1.0
CA B:VAL11 3.8 11.2 1.0
CA B:ALA67 3.8 12.5 1.0
CB B:ALA67 3.9 13.9 1.0
C B:VAL11 4.0 10.6 1.0
CB B:THR12 4.0 13.0 1.0
O B:THR12 4.1 11.2 1.0
CA B:THR12 4.1 10.9 1.0
OG1 B:THR12 4.2 16.1 1.0
CG1 B:VAL11 4.3 14.6 1.0
C B:THR12 4.6 11.9 1.0
N B:ALA67 4.6 11.8 1.0
C B:ALA67 4.8 12.3 1.0
CG2 B:VAL11 4.9 13.9 1.0
C2 B:GOL205 5.0 17.5 0.5

Reference:

A.K.Ghosh, A.Grillo, J.Raghavaiah, S.Kovela, M.E.Johnson, D.W.Kneller, Y.F.Wang, S.I.Hattori, N.Higashi-Kuwata, I.T.Weber, H.Mitsuya. Design, Synthesis, and X-Ray Studies of Potent Hiv-1 Protease Inhibitors with P2-Carboxamide Functionalities. Acs Med.Chem.Lett. V. 11 1965 2020.
ISSN: ISSN 1948-5875
PubMed: 33062180
DOI: 10.1021/ACSMEDCHEMLETT.9B00670
Page generated: Sat Dec 12 14:16:33 2020

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