Atomistry » Fluorine » PDB 6c0u-6cr2 » 6cdl
Atomistry »
  Fluorine »
    PDB 6c0u-6cr2 »
      6cdl »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy