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Fluorine in PDB 6b3h: Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide

Enzymatic activity of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide

All present enzymatic activity of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide, PDB code: 6b3h was solved by H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 1.62
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.430, 86.200, 46.230, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.9

Other elements in 6b3h:

The structure of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide (pdb code 6b3h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide, PDB code: 6b3h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6b3h

Go back to Fluorine Binding Sites List in 6b3h
Fluorine binding site 1 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F101

b:23.1
occ:1.00
 F2 A:CN4101 0.0 23.1 1.0
C10 A:CN4101 1.4 19.8 1.0
C9 A:CN4101 2.3 17.4 1.0
C11 A:CN4101 2.3 19.1 1.0
C8 A:CN4101 2.8 18.8 1.0
C7 A:CN4101 3.1 18.2 1.0
CB A:ASP30 3.2 19.8 1.0
CD1 A:LEU76 3.3 19.1 1.0
N A:ASP30 3.4 17.2 1.0
C12 A:CN4101 3.6 17.9 1.0
C14 A:CN4101 3.6 15.4 1.0
CA A:ASP30 3.7 17.0 1.0
O A:ASP30 3.7 18.6 1.0
OD2 A:ASP30 3.7 33.4 1.0
C A:ASP30 3.9 20.0 1.0
CG A:ASP30 4.0 29.4 1.0
C13 A:CN4101 4.1 17.0 1.0
C3 A:CN4101 4.4 21.4 1.0
CG2 A:VAL32 4.4 18.6 1.0
C A:ASP29 4.5 18.6 1.0
CD1 A:ILE47 4.5 17.5 1.0
CG2 A:ILE47 4.5 17.1 1.0
CG A:LEU76 4.6 18.4 1.0
CB A:ASP29 4.7 16.9 1.0
N A:ASP29 4.7 14.4 1.0
N2 A:CN4101 4.8 16.0 1.0
N A:THR31 4.9 17.6 1.0
CA A:ASP29 4.9 14.9 1.0
O A:HOH217 4.9 18.7 1.0

Fluorine binding site 2 out of 6 in 6b3h

Go back to Fluorine Binding Sites List in 6b3h
Fluorine binding site 2 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F101

b:21.1
occ:1.00
 F1 A:CN4101 0.0 21.1 1.0
C27 A:CN4101 1.4 19.6 1.0
C26 A:CN4101 2.3 18.6 1.0
C28 A:CN4101 2.4 17.6 1.0
C B:CN4101 3.1 18.2 1.0
C1 B:CN4101 3.3 19.3 1.0
C6 B:CN4101 3.5 21.6 1.0
C5 B:CN4101 3.6 20.8 1.0
CG2 B:VAL82 3.6 24.6 1.0
C25 A:CN4101 3.6 17.9 1.0
C29 A:CN4101 3.6 19.5 1.0
CD2 B:LEU23 3.7 22.0 1.0
CD1 B:ILE84 3.8 28.0 1.0
O A:GLY27 3.9 17.6 1.0
O1 B:CN4101 4.1 17.3 1.0
C24 A:CN4101 4.1 18.3 1.0
CG1 B:ILE84 4.2 17.9 1.0
N1 B:CN4101 4.3 18.0 1.0
C A:GLY27 4.6 17.9 1.0
C4 B:CN4101 4.7 21.5 1.0
S B:CN4101 4.7 19.9 1.0
OD2 B:ASP25 4.7 24.5 1.0
O A:HOH206 4.8 36.7 1.0
N B:CN4101 4.8 19.4 1.0
CA A:GLY27 4.9 14.8 1.0

Fluorine binding site 3 out of 6 in 6b3h

Go back to Fluorine Binding Sites List in 6b3h
Fluorine binding site 3 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F101

b:25.7
occ:1.00
 F A:CN4101 0.0 25.7 1.0
C21 A:CN4101 1.4 23.6 1.0
C22 A:CN4101 2.4 23.0 1.0
C20 A:CN4101 2.4 22.0 1.0
C23 A:CN4101 3.6 18.7 1.0
C19 A:CN4101 3.6 20.8 1.0
O B:PRO81 4.0 21.0 1.0
C18 A:CN4101 4.1 17.2 1.0
CB B:PRO81 4.1 20.6 1.0
O B:HOH212 4.3 32.5 1.0
CA B:PRO81 4.5 18.9 1.0
C B:PRO81 4.6 21.5 1.0

Fluorine binding site 4 out of 6 in 6b3h

Go back to Fluorine Binding Sites List in 6b3h
Fluorine binding site 4 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:20.4
occ:1.00
 F2 B:CN4101 0.0 20.4 1.0
C10 B:CN4101 1.4 18.7 1.0
C9 B:CN4101 2.3 16.6 1.0
C11 B:CN4101 2.3 18.5 1.0
C8 B:CN4101 2.8 17.0 1.0
C7 B:CN4101 3.2 18.3 1.0
CD1 B:ILE84 3.4 28.0 1.0
C12 B:CN4101 3.6 16.3 1.0
C14 B:CN4101 3.6 17.4 1.0
CG1 B:VAL32 3.7 16.3 1.0
CB B:ALA28 3.8 14.3 1.0
CG2 B:ILE84 3.8 18.3 1.0
CD1 A:ILE50 3.9 36.6 1.0
CG1 A:ILE50 3.9 21.8 1.0
C13 B:CN4101 4.1 17.2 1.0
C B:CN4101 4.1 18.2 1.0
CB B:ILE84 4.2 16.0 1.0
N1 B:CN4101 4.3 18.0 1.0
CG1 B:ILE84 4.3 17.9 1.0
C3 B:CN4101 4.4 19.4 1.0
OD2 B:ASP25 4.5 24.5 1.0
O B:ASP30 4.7 16.0 1.0
CA B:ALA28 4.7 12.6 1.0
CD1 B:ILE47 4.7 20.8 1.0
N2 B:CN4101 4.8 17.6 1.0
CB B:VAL32 4.9 16.5 1.0
CB A:ILE50 4.9 20.6 1.0

Fluorine binding site 5 out of 6 in 6b3h

Go back to Fluorine Binding Sites List in 6b3h
Fluorine binding site 5 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:39.0
occ:1.00
 F1 B:CN4101 0.0 39.0 1.0
C27 B:CN4101 1.4 33.9 1.0
C26 B:CN4101 2.3 33.1 1.0
C28 B:CN4101 2.4 31.4 1.0
O A:HOH220 3.1 35.0 1.0
O A:HOH242 3.6 37.9 1.0
C25 B:CN4101 3.6 29.1 1.0
C29 B:CN4101 3.6 27.2 1.0
NH1 A:ARG8 4.1 23.3 1.0
C24 B:CN4101 4.1 25.0 1.0
O A:PRO81 4.2 24.5 1.0
O A:HOH247 4.3 40.0 1.0
CB A:VAL82 4.3 24.7 1.0
O A:HOH219 4.4 37.1 1.0
CG2 A:VAL82 4.4 25.3 1.0
O A:HOH249 4.9 40.8 1.0
CZ A:ARG8 5.0 30.0 1.0

Fluorine binding site 6 out of 6 in 6b3h

Go back to Fluorine Binding Sites List in 6b3h
Fluorine binding site 6 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Hiv Protease Complexed with N-(2-(2-((6R,9S)-2,2- Dioxido-2-Thia-1,7-Diazabicyclo[4.3.1]Decan-9-Yl)Ethyl)-3- Fluorophenyl)-3,3-Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:33.9
occ:1.00
 F B:CN4101 0.0 33.9 1.0
C21 B:CN4101 1.4 25.8 1.0
C22 B:CN4101 2.3 22.8 1.0
C20 B:CN4101 2.3 26.0 1.0
O B:CN4101 3.3 22.1 1.0
C23 B:CN4101 3.6 20.2 1.0
C19 B:CN4101 3.6 21.6 1.0
N B:ILE50 3.8 18.1 1.0
CB B:ILE50 3.9 22.8 1.0
C2 B:CN4101 3.9 19.6 1.0
C3 B:CN4101 4.0 19.4 1.0
CA B:ILE50 4.0 19.2 1.0
C4 B:CN4101 4.0 21.5 1.0
CD1 A:ILE84 4.1 34.2 1.0
C18 B:CN4101 4.1 19.3 1.0
S B:CN4101 4.2 19.9 1.0
CG2 A:ILE84 4.2 23.1 1.0
CG1 A:VAL82 4.3 25.3 1.0
CD1 B:ILE50 4.3 32.2 1.0
C B:GLY49 4.4 20.9 1.0
CG1 B:ILE50 4.5 24.9 1.0
OG1 A:THR80 4.5 19.7 1.0
N1 B:CN4101 4.5 18.0 1.0
CG A:PRO81 4.8 28.1 1.0
CD A:PRO81 4.8 23.5 1.0
CA B:GLY49 4.9 16.8 1.0
OD2 A:ASP25 4.9 31.0 1.0

Reference:

C.J.Bungard, P.D.Williams, J.Schulz, C.M.Wiscount, M.K.Holloway, H.M.Loughran, J.J.Manikowski, H.P.Su, D.J.Bennett, L.Chang, X.J.Chu, A.Crespo, M.P.Dwyer, K.Keertikar, G.J.Morriello, A.W.Stamford, S.T.Waddell, B.Zhong, B.Hu, T.Ji, T.L.Diamond, C.Bahnck-Teets, S.S.Carroll, J.F.Fay, X.Min, W.Morris, J.E.Ballard, M.D.Miller, J.A.Mccauley. Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent Hiv-1 Protease Inhibitors. Acs Med Chem Lett V. 8 1292 2017.
ISSN: ISSN 1948-5875
PubMed: 29259750
DOI: 10.1021/ACSMEDCHEMLETT.7B00386
Page generated: Thu Aug 1 17:57:35 2024

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