Fluorine 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:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 4 in 6cdj

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

b:16.5
occ:0.55
F61 A:GR8201 0.0 16.5 0.6
C34 A:GR8201 1.4 12.9 0.6
C35 A:GR8201 2.3 13.0 0.6
C33 A:GR8201 2.4 10.9 0.6
O B:HOH285 2.6 18.5 0.5
C15 A:GR8201 3.0 13.9 0.5
O3 A:GOL204 3.4 31.0 0.5
C29 A:GR8201 3.4 12.6 0.6
O1 A:GOL204 3.5 29.2 0.5
CG2 B:VAL82 3.6 29.3 0.5
C36 A:GR8201 3.6 12.4 0.6
NH2 B:ARG8 3.6 18.0 0.6
C38 A:GR8201 3.7 9.2 0.6
NH1 B:ARG8 3.7 21.0 0.6
CZ B:ARG8 3.8 18.0 0.6
CG1 B:VAL82 3.8 28.5 0.6
O A:HOH350 3.9 15.8 0.5
O A:HOH344 3.9 16.8 1.0
CG2 B:VAL82 4.0 21.1 0.6
C30 A:GR8201 4.0 12.8 0.6
C3 A:GOL204 4.1 27.2 0.5
C37 A:GR8201 4.1 10.7 0.6
C31 A:GR8201 4.1 11.7 0.6
CB B:VAL82 4.3 20.9 0.5
C13 A:GR8201 4.3 9.2 0.5
C12 A:GR8201 4.4 10.6 0.5
C1 A:GOL204 4.4 32.6 0.5
CB B:VAL82 4.6 18.4 0.6
C2 A:GOL204 4.6 32.7 0.5
F62 A:GR8201 4.7 14.9 0.6
O28 A:GR8201 4.7 11.0 0.6
CG1 B:VAL82 4.7 19.5 0.5
NE B:ARG8 4.7 20.0 0.6
CD2 B:LEU23 4.8 15.2 1.0
O A:GLY27 4.8 10.4 1.0
C32 A:GR8201 4.9 9.7 0.6

Fluorine binding site 2 out of 4 in 6cdj

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

b:16.8
occ:0.45
F61 A:GR8201 0.0 16.8 0.5
C34 A:GR8201 1.4 12.6 0.5
O B:HOH231 2.4 23.0 0.6
C35 A:GR8201 2.4 12.4 0.5
C33 A:GR8201 2.4 11.2 0.5
O A:HOH388 2.7 18.4 0.5
C15 A:GR8201 3.2 16.5 0.6
CG2 A:VAL82 3.2 31.0 1.0
C29 A:GR8201 3.4 12.7 0.5
NH1 A:ARG8 3.5 22.0 0.6
NH2 A:ARG8 3.6 24.9 0.6
C36 A:GR8201 3.6 10.9 0.5
C38 A:GR8201 3.6 9.2 0.5
CZ A:ARG8 3.7 24.0 0.6
O A:HOH386 3.9 31.8 0.6
O B:HOH245 3.9 15.1 0.6
C31 A:GR8201 4.0 13.2 0.5
C30 A:GR8201 4.0 14.0 0.5
O B:HOH241 4.1 16.1 1.0
C37 A:GR8201 4.1 10.4 0.5
CB A:VAL82 4.2 22.7 1.0
C12 A:GR8201 4.3 12.6 0.6
C13 A:GR8201 4.4 12.9 0.6
CG1 A:VAL82 4.6 26.6 1.0
NE A:ARG8 4.6 21.5 0.6
O28 A:GR8201 4.7 12.2 0.5
F62 A:GR8201 4.7 13.9 0.5
O B:GLY48 4.8 15.4 0.6
C32 A:GR8201 4.9 10.2 0.5
O B:GLY27 4.9 11.7 1.0
CD2 A:LEU23 5.0 17.0 1.0
CZ A:ARG8 5.0 21.6 0.5

Fluorine binding site 3 out of 4 in 6cdj

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

b:14.9
occ:0.55
F62 A:GR8201 0.0 14.9 0.6
C36 A:GR8201 1.4 12.4 0.6
CG B:PRO81 2.0 23.0 0.5
C35 A:GR8201 2.3 13.0 0.6
C37 A:GR8201 2.4 10.7 0.6
CD B:PRO81 2.9 24.2 0.6
CA A:GLY49 2.9 21.3 0.6
CD B:PRO81 2.9 24.1 0.5
C A:GLY49 3.0 17.8 0.6
CG B:PRO81 3.0 24.1 0.6
N A:ILE50 3.0 14.9 0.6
C14 A:GR8201 3.1 11.4 0.5
CA A:GLY49 3.2 19.6 0.5
C A:GLY49 3.2 13.4 0.5
CB B:PRO81 3.3 21.9 0.5
N A:ILE50 3.4 14.4 0.5
C34 A:GR8201 3.6 12.9 0.6
CB B:PRO81 3.6 21.7 0.6
C38 A:GR8201 3.6 9.2 0.6
CA A:ILE50 3.7 14.9 0.5
O A:GLY49 3.7 16.7 0.6
O A:GLY49 3.8 17.2 0.5
C15 A:GR8201 3.8 13.9 0.5
C13 A:GR8201 3.9 9.2 0.5
CA A:ILE50 4.0 13.6 0.6
CG1 A:ILE50 4.0 21.3 1.0
C33 A:GR8201 4.1 10.9 0.6
N B:PRO81 4.1 21.3 0.5
N B:PRO81 4.1 20.9 0.6
N A:GLY49 4.2 19.4 0.6
N A:GLY49 4.3 17.5 0.5
CA B:PRO81 4.3 22.2 0.5
CB A:ILE50 4.4 17.2 1.0
CA B:PRO81 4.4 22.0 0.6
C12 A:GR8201 4.5 10.6 0.5
O A:GLY48 4.5 32.3 0.6
O A:GLY48 4.6 12.2 0.5
OG1 B:THR80 4.6 16.7 1.0
O22 A:GR8201 4.6 12.4 0.6
F61 A:GR8201 4.7 16.5 0.6
N B:VAL82 4.7 18.1 1.0
O A:HOH302 4.7 16.7 1.0
CG2 B:VAL82 4.7 21.1 0.6
O10 A:GR8201 4.8 11.2 0.5
C B:PRO81 4.8 20.5 0.6
C32 A:GR8201 4.8 9.7 0.6
C3 A:GOL204 4.8 27.2 0.5
C A:GLY48 4.8 17.2 0.6
O9 A:GR8201 4.8 12.2 0.6
C A:GLY48 4.8 15.8 0.5
C A:ILE50 4.9 16.2 0.5
C B:PRO81 5.0 20.3 0.5
CD1 B:ILE84 5.0 13.8 0.6
CD1 A:ILE50 5.0 29.5 1.0

Fluorine binding site 4 out of 4 in 6cdj

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

b:13.9
occ:0.45
F62 A:GR8201 0.0 13.9 0.5
C36 A:GR8201 1.3 10.9 0.5
CG A:PRO81 2.2 17.8 0.6
C35 A:GR8201 2.3 12.4 0.5
C37 A:GR8201 2.3 10.4 0.5
CD A:PRO81 2.9 17.8 0.6
N B:ILE50 2.9 16.7 0.5
O B:GLY49 3.0 17.8 0.6
O B:HOH231 3.0 23.0 0.6
C B:GLY49 3.0 17.7 0.6
CD A:PRO81 3.1 15.8 0.5
C B:GLY49 3.1 16.0 0.5
CG A:PRO81 3.1 16.4 0.5
N B:ILE50 3.3 16.2 0.6
CA B:ILE50 3.4 15.5 0.6
CB A:PRO81 3.5 16.7 0.5
C14 A:GR8201 3.5 15.0 0.6
CB A:PRO81 3.6 17.8 0.6
CA B:GLY49 3.6 21.5 0.5
C34 A:GR8201 3.6 12.6 0.5
O B:GLY49 3.6 17.4 0.5
C38 A:GR8201 3.6 9.2 0.5
CA B:ILE50 3.6 16.3 0.5
CA B:GLY49 3.7 19.8 0.6
C15 A:GR8201 3.8 16.5 0.6
O B:GLY48 4.1 21.2 0.5
C33 A:GR8201 4.1 11.2 0.5
N A:PRO81 4.1 15.0 0.6
CB B:ILE50 4.1 18.3 1.0
N A:PRO81 4.2 14.7 0.5
C13 A:GR8201 4.2 12.9 0.6
N B:GLY49 4.2 18.9 0.6
CG1 B:ILE50 4.4 26.6 1.0
O B:GLY48 4.4 15.4 0.6
CA A:PRO81 4.4 15.2 0.5
CA A:PRO81 4.5 16.2 0.6
C B:ILE50 4.5 14.3 0.6
OG1 A:THR80 4.6 14.3 1.0
N B:GLY49 4.6 22.7 0.5
C B:GLY48 4.6 16.5 0.6
C12 A:GR8201 4.6 12.6 0.6
O22 A:GR8201 4.7 10.2 0.5
N A:VAL82 4.7 14.0 1.0
F61 A:GR8201 4.7 16.8 0.5
C B:GLY48 4.8 20.5 0.5
O A:HOH302 4.8 16.7 1.0
CG2 A:VAL82 4.8 31.0 1.0
O9 A:GR8201 4.8 10.6 0.5
C A:PRO81 4.8 14.7 0.5
O B:HOH216 4.9 29.1 1.0
O10 A:GR8201 4.9 12.9 0.6
C32 A:GR8201 4.9 10.2 0.5
O B:ILE50 4.9 16.8 0.6
C A:PRO81 4.9 16.1 0.6
C B:ILE50 5.0 15.0 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: Sun Dec 13 12:46:33 2020

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