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Fluorine 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:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6cdl

Go back to Fluorine Binding Sites List in 6cdl
Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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
B:F201

b:14.1
occ:0.50
 F61 B:GR5201 0.0 14.1 0.5
C34 B:GR5201 1.4 11.0 0.5
NH1 A:ARG8 2.3 31.8 0.5
C35 B:GR5201 2.4 11.8 0.5
C33 B:GR5201 2.4 11.0 0.5
C15 B:GR5201 3.1 15.4 0.5
CZ A:ARG8 3.1 25.4 0.5
NH2 A:ARG8 3.4 34.4 0.5
NH2 A:ARG8 3.4 32.5 0.5
C42 B:GR5201 3.5 14.7 0.5
C41 B:GR5201 3.5 12.8 0.5
CG1 A:VAL82 3.5 23.2 0.5
CG1 A:VAL82 3.6 17.6 0.5
C36 B:GR5201 3.6 10.3 0.5
NH1 A:ARG8 3.6 18.8 0.5
O A:HOH654 3.6 24.3 0.2
C38 B:GR5201 3.7 8.9 0.5
CZ A:ARG8 3.7 19.4 0.5
O B:HOH352 3.8 17.1 0.5
O A:HOH624 3.9 15.6 1.0
CG2 A:VAL82 4.0 19.8 0.5
C37 B:GR5201 4.2 8.8 0.5
NE A:ARG8 4.2 23.6 0.5
CB A:VAL82 4.3 15.6 0.5
C13 B:GR5201 4.3 12.3 0.5
C12 B:GR5201 4.3 10.7 0.5
CB A:VAL82 4.4 15.2 0.5
NE A:ARG8 4.6 12.8 0.5
F62 B:GR5201 4.7 13.1 0.5
CG2 A:VAL82 4.7 16.4 0.5
O43 B:GR5201 4.7 15.7 0.5
O B:GLY27 4.8 10.5 1.0
O23 B:GR5201 4.8 11.7 0.5
CD2 A:LEU23 4.8 15.8 1.0
C25 B:GR5201 4.8 12.6 0.5
O B:GLY48 4.9 17.5 1.0
C32 B:GR5201 4.9 9.0 0.5

Fluorine binding site 2 out of 4 in 6cdl

Go back to Fluorine Binding Sites List in 6cdl
Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F 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:F201

b:14.8
occ:0.50
 F61 B:GR5201 0.0 14.8 0.5
C34 B:GR5201 1.4 10.4 0.5
NH2 B:ARG8 2.3 22.7 0.5
C33 B:GR5201 2.3 8.8 0.5
C35 B:GR5201 2.4 12.4 0.5
C15 B:GR5201 3.0 12.0 0.5
C42 B:GR5201 3.4 15.2 0.5
CZ B:ARG8 3.4 24.2 0.5
C41 B:GR5201 3.5 12.8 0.5
CG2 B:VAL82 3.6 26.5 0.5
C38 B:GR5201 3.6 9.8 0.5
C36 B:GR5201 3.6 11.4 0.5
NH1 B:ARG8 3.7 26.5 0.5
NH2 B:ARG8 3.7 22.6 0.5
O A:HOH695 3.8 23.9 0.2
O A:HOH640 3.8 15.9 0.5
CZ B:ARG8 3.9 19.6 0.5
O B:HOH303 3.9 17.7 1.0
NH1 B:ARG8 4.0 33.3 0.5
O A:HOH657 4.1 22.1 0.2
C37 B:GR5201 4.1 10.6 0.5
CG1 B:VAL82 4.1 26.4 0.5
C13 B:GR5201 4.3 9.1 0.5
C12 B:GR5201 4.3 9.4 0.5
CB B:VAL82 4.3 21.8 0.5
NE B:ARG8 4.4 23.6 0.5
CB B:VAL82 4.4 20.8 0.5
O43 B:GR5201 4.7 14.2 0.5
CD2 B:LEU23 4.7 12.6 1.0
O A:GLY27 4.7 9.6 1.0
CG1 B:VAL82 4.7 29.5 0.5
F62 B:GR5201 4.8 17.9 0.5
NE B:ARG8 4.8 15.5 0.5
O23 B:GR5201 4.8 11.8 0.5
C32 B:GR5201 4.9 9.0 0.5
C25 B:GR5201 4.9 12.8 0.5
CG2 B:VAL82 5.0 28.7 0.5

Fluorine binding site 3 out of 4 in 6cdl

Go back to Fluorine Binding Sites List in 6cdl
Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F binding site number 3 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:F201

b:13.1
occ:0.50
 F62 B:GR5201 0.0 13.1 0.5
C36 B:GR5201 1.3 10.3 0.5
CG A:PRO81 2.3 17.8 0.5
C35 B:GR5201 2.3 11.8 0.5
C37 B:GR5201 2.4 8.8 0.5
C B:GLY49 3.0 17.4 1.0
N B:ILE50 3.1 16.1 0.5
CD A:PRO81 3.1 16.1 0.5
O B:GLY49 3.1 17.2 1.0
CG A:PRO81 3.1 15.1 0.5
N B:ILE50 3.2 13.9 0.5
CD A:PRO81 3.2 16.1 0.5
CA B:ILE50 3.3 12.2 0.5
C14 B:GR5201 3.4 16.8 0.5
CB A:PRO81 3.5 17.6 0.5
CA B:ILE50 3.5 14.5 0.5
C34 B:GR5201 3.6 11.0 0.5
C38 B:GR5201 3.6 8.9 0.5
CB A:PRO81 3.7 17.4 0.5
CA B:GLY49 3.7 18.6 1.0
CG1 B:ILE50 3.9 14.7 0.5
C15 B:GR5201 3.9 15.4 0.5
CG1 A:VAL82 4.0 23.2 0.5
C33 B:GR5201 4.1 11.0 0.5
CB B:ILE50 4.1 16.8 0.5
O B:GLY48 4.2 17.5 1.0
C13 B:GR5201 4.2 12.3 0.5
CB B:ILE50 4.2 14.8 0.5
N A:PRO81 4.3 13.5 1.0
O B:HOH337 4.5 25.8 1.0
N B:GLY49 4.5 17.0 1.0
C B:ILE50 4.5 9.2 0.5
CA A:PRO81 4.5 14.3 0.5
C B:GLY48 4.6 13.7 1.0
CG2 A:VAL82 4.6 19.8 0.5
CA A:PRO81 4.6 14.3 0.5
C12 B:GR5201 4.6 10.7 0.5
F61 B:GR5201 4.7 14.1 0.5
O22 B:GR5201 4.8 8.1 0.5
OG1 A:THR80 4.8 11.4 1.0
N A:VAL82 4.8 12.0 1.0
C B:ILE50 4.8 14.3 0.5
O10 B:GR5201 4.8 13.0 0.5
O B:HOH302 4.9 17.6 1.0
O B:HOH397 4.9 36.2 1.0
C32 B:GR5201 4.9 9.0 0.5
CG1 B:ILE50 4.9 20.0 0.5
CD1 B:ILE50 4.9 21.7 0.5
O9 B:GR5201 4.9 8.7 0.5
O B:ILE50 4.9 10.6 0.5

Fluorine binding site 4 out of 4 in 6cdl

Go back to Fluorine Binding Sites List in 6cdl
Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F binding site number 4 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:F201

b:17.9
occ:0.50
 F62 B:GR5201 0.0 17.9 0.5
C36 B:GR5201 1.4 11.4 0.5
CG B:PRO81 2.1 23.1 0.5
C37 B:GR5201 2.4 10.6 0.5
C35 B:GR5201 2.4 12.4 0.5
N A:ILE50 2.9 12.8 0.5
CA A:GLY49 2.9 22.4 1.0
CD B:PRO81 2.9 22.4 0.5
CD B:PRO81 2.9 22.8 0.5
C A:GLY49 3.0 16.4 1.0
CG B:PRO81 3.0 21.3 0.5
N A:ILE50 3.0 15.0 0.5
C14 B:GR5201 3.2 11.2 0.5
CB B:PRO81 3.3 22.6 0.5
CB B:PRO81 3.4 22.4 0.5
C34 B:GR5201 3.6 10.4 0.5
C38 B:GR5201 3.6 9.8 0.5
CA A:ILE50 3.7 13.7 0.5
C15 B:GR5201 3.7 12.0 0.5
O A:GLY49 3.7 14.7 1.0
CG1 A:ILE50 3.8 17.8 1.0
CA A:ILE50 3.9 9.3 0.5
C13 B:GR5201 4.0 9.1 0.5
N B:PRO81 4.0 19.7 1.0
C33 B:GR5201 4.1 8.8 0.5
N A:GLY49 4.2 17.9 1.0
CA B:PRO81 4.3 20.8 0.5
CA B:PRO81 4.3 21.0 0.5
CB A:ILE50 4.4 13.8 1.0
CG1 B:VAL82 4.5 26.4 0.5
OG1 B:THR80 4.5 15.3 1.0
C12 B:GR5201 4.6 9.4 0.5
O A:GLY48 4.6 13.2 1.0
O B:HOH302 4.6 17.6 1.0
N B:VAL82 4.6 18.1 1.0
O10 B:GR5201 4.7 10.1 0.5
O9 B:GR5201 4.8 11.4 0.5
F61 B:GR5201 4.8 14.8 0.5
O22 B:GR5201 4.8 12.1 0.5
C A:GLY48 4.8 12.1 1.0
C B:PRO81 4.8 20.9 1.0
C32 B:GR5201 4.9 9.0 0.5
CD1 A:ILE50 4.9 24.4 1.0
CD1 B:ILE84 4.9 12.7 0.5
C A:ILE50 5.0 13.6 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: Tue Jul 15 10:22:30 2025

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