Atomistry » Fluorine » PDB 6c0t-6cqh » 6cdl
Atomistry »
  Fluorine »
    PDB 6c0t-6cqh »
      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: Thu Aug 1 18:30:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy