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Fluorine in PDB 6b38: Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide

Enzymatic activity of Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide

All present enzymatic activity of Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide, PDB code: 6b38 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) 21.44 / 1.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.330, 85.780, 46.550, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 19.6

Other elements in 6b38:

The structure of Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide (pdb code 6b38). 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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide, PDB code: 6b38:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6b38

Go back to Fluorine Binding Sites List in 6b38
Fluorine binding site 1 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:17.2
occ:0.50
 F37 B:CKM101 0.0 17.2 0.5
C28 B:CKM101 1.3 13.8 0.5
C27 B:CKM101 2.4 10.7 0.5
C29 B:CKM101 2.4 12.8 0.5
O5 B:CKM102 2.8 41.5 0.5
C39 B:CKM102 2.8 37.6 0.5
O B:CKM101 3.2 16.8 0.5
C11 B:CKM101 3.4 17.1 0.5
CD1 A:ILE84 3.4 25.2 1.0
N B:ILE50 3.4 18.5 1.0
CA B:ILE50 3.5 18.7 1.0
C30 B:CKM101 3.6 13.4 0.5
C26 B:CKM101 3.6 11.1 0.5
C38 B:CKM102 3.7 36.8 0.5
CB B:ILE50 3.7 22.0 1.0
CD1 B:ILE50 3.7 29.4 1.0
N3 B:CKM102 3.8 36.2 0.5
F B:CKM102 3.9 27.5 0.5
C B:GLY49 4.0 21.1 1.0
S B:CKM102 4.0 40.9 0.5
C25 B:CKM101 4.1 12.1 0.5
C10 B:CKM101 4.1 19.4 0.5
C6 B:CKM101 4.2 17.1 0.5
C2 B:CKM101 4.2 13.4 0.5
S B:CKM101 4.3 16.7 0.5
CG1 B:ILE50 4.3 24.0 1.0
OG1 A:THR80 4.4 16.6 1.0
CD A:PRO81 4.4 22.4 1.0
CG1 A:VAL82 4.4 22.1 1.0
O B:GLY49 4.5 19.6 1.0
C1 B:CKM101 4.5 16.0 0.5
CG A:PRO81 4.5 27.5 1.0
CA B:GLY49 4.5 17.9 1.0
CG1 A:ILE84 4.6 16.8 1.0
N3 B:CKM101 4.9 14.5 0.5
CG2 B:ILE50 4.9 22.7 1.0
C B:ILE50 5.0 23.8 1.0

Fluorine binding site 2 out of 6 in 6b38

Go back to Fluorine Binding Sites List in 6b38
Fluorine binding site 2 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:24.6
occ:0.50
 F36 B:CKM101 0.0 24.6 0.5
C33 B:CKM101 1.3 21.1 0.5
C32 B:CKM101 2.3 18.9 0.5
C34 B:CKM101 2.4 16.8 0.5
O A:HOH242 3.1 40.3 1.0
C31 B:CKM101 3.6 19.0 0.5
C35 B:CKM101 3.6 12.1 0.5
O A:HOH250 3.6 35.6 1.0
NH1 A:ARG8 3.8 24.3 1.0
C24 B:CKM101 4.1 15.7 0.5
CB A:VAL82 4.3 22.2 1.0
CG2 A:VAL82 4.3 22.6 1.0
O A:HOH233 4.3 43.6 1.0
O A:PRO81 4.5 24.2 1.0
CZ A:ARG8 4.7 32.4 1.0

Fluorine binding site 3 out of 6 in 6b38

Go back to Fluorine Binding Sites List in 6b38
Fluorine binding site 3 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:15.9
occ:0.50
 F B:CKM101 0.0 15.9 0.5
C10 B:CKM102 0.8 42.1 0.5
C18 B:CKM101 1.3 12.8 0.5
C11 B:CKM102 1.9 41.4 0.5
C9 B:CKM102 1.9 42.0 0.5
C13 B:CKM101 2.4 12.6 0.5
C17 B:CKM101 2.4 11.9 0.5
C12 B:CKM101 2.8 11.8 0.5
C6 B:CKM102 3.1 41.0 0.5
C8 B:CKM102 3.1 42.1 0.5
CD1 B:ILE84 3.3 25.6 1.0
C4 B:CKM101 3.3 12.9 0.5
CD1 A:ILE50 3.4 40.2 1.0
C7 B:CKM102 3.5 41.7 0.5
C14 B:CKM101 3.6 12.4 0.5
C16 B:CKM101 3.6 12.1 0.5
CG2 B:ILE84 3.9 17.1 1.0
C39 B:CKM101 3.9 18.5 0.5
CG1 B:VAL32 3.9 21.3 1.0
CB B:ALA28 3.9 12.5 1.0
F37 B:CKM102 4.0 35.1 0.5
C15 B:CKM101 4.1 13.2 0.5
N3 B:CKM101 4.2 14.5 0.5
CG1 B:ILE84 4.3 15.8 1.0
CB B:ILE84 4.4 14.5 1.0
C2 B:CKM101 4.4 13.4 0.5
OD2 B:ASP25 4.4 29.6 1.0
CG1 A:ILE50 4.5 26.9 1.0
S B:CKM102 4.6 40.9 0.5
C1 B:CKM102 4.7 34.7 0.5
C38 B:CKM101 4.7 15.5 0.5
CB A:ILE50 4.8 24.1 1.0
O B:CKM102 4.8 41.9 0.5
N19 B:CKM101 4.8 11.2 0.5
C B:CKM102 4.8 36.3 0.5
CA B:ALA28 4.9 11.4 1.0
CD1 B:ILE47 5.0 22.3 1.0

Fluorine binding site 4 out of 6 in 6b38

Go back to Fluorine Binding Sites List in 6b38
Fluorine binding site 4 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F102

b:35.1
occ:0.50
 F37 B:CKM102 0.0 35.1 0.5
C28 B:CKM102 1.3 31.2 0.5
C29 B:CKM102 2.3 29.5 0.5
C27 B:CKM102 2.4 28.5 0.5
O5 B:CKM101 2.8 15.0 0.5
C39 B:CKM101 3.0 18.5 0.5
CD1 B:ILE84 3.1 25.6 1.0
O B:CKM102 3.2 41.9 0.5
C11 B:CKM102 3.3 41.4 0.5
CD1 A:ILE50 3.5 40.2 1.0
C30 B:CKM102 3.6 27.5 0.5
C26 B:CKM102 3.6 25.7 0.5
CG1 A:ILE50 3.6 26.9 1.0
N A:ILE50 3.6 18.8 1.0
CD B:PRO81 3.7 28.9 1.0
C38 B:CKM101 3.7 15.5 0.5
N3 B:CKM101 3.7 14.5 0.5
S B:CKM101 3.9 16.7 0.5
F B:CKM101 4.0 15.9 0.5
CB A:ILE50 4.0 24.1 1.0
C2 B:CKM102 4.0 32.5 0.5
C10 B:CKM102 4.1 42.1 0.5
C25 B:CKM102 4.1 25.8 0.5
C6 B:CKM102 4.1 41.0 0.5
S B:CKM102 4.1 40.9 0.5
OG1 B:THR80 4.2 23.7 1.0
CG B:PRO81 4.3 33.4 1.0
C1 B:CKM102 4.3 34.7 0.5
CA A:ILE50 4.4 19.8 1.0
CG1 B:ILE84 4.4 15.8 1.0
CA A:GLY49 4.4 20.2 1.0
C A:GLY49 4.4 21.0 1.0
N3 B:CKM102 4.7 36.2 0.5
N B:PRO81 4.8 25.9 1.0
O B:CKM101 4.9 16.8 0.5
CB B:PRO81 4.9 27.3 1.0
C12 B:CKM101 4.9 11.8 0.5

Fluorine binding site 5 out of 6 in 6b38

Go back to Fluorine Binding Sites List in 6b38
Fluorine binding site 5 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F102

b:30.9
occ:0.50
 F36 B:CKM102 0.0 30.9 0.5
C33 B:CKM102 1.3 29.8 0.5
C32 B:CKM102 2.4 26.9 0.5
C34 B:CKM102 2.4 29.8 0.5
CG1 B:VAL82 3.2 25.7 1.0
O B:HOH270 3.4 41.4 1.0
NH2 B:ARG8 3.5 30.0 1.0
C31 B:CKM102 3.6 26.6 0.5
C35 B:CKM102 3.6 27.6 0.5
C24 B:CKM102 4.1 25.8 0.5
CZ B:ARG8 4.4 42.4 1.0
CB B:VAL82 4.7 24.3 1.0
O B:PRO81 4.8 26.8 1.0
NH1 B:ARG8 4.8 31.2 1.0

Fluorine binding site 6 out of 6 in 6b38

Go back to Fluorine Binding Sites List in 6b38
Fluorine binding site 6 out of 6 in the Crystal Structure of Hiv Protease Complexed with N-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-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-(3-Fluoro-2-(2- ((2S,6R)-6-Methyl-1-(Phenylsulfonyl)Piperazin-2-Yl)Ethyl)Phenyl)-3,3- Bis(4-Fluorophenyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F102

b:27.5
occ:0.50
 F B:CKM102 0.0 27.5 0.5
C10 B:CKM101 0.9 19.4 0.5
C18 B:CKM102 1.3 26.0 0.5
C11 B:CKM101 1.7 17.1 0.5
C9 B:CKM101 2.2 18.3 0.5
C17 B:CKM102 2.3 26.5 0.5
C13 B:CKM102 2.4 23.7 0.5
C12 B:CKM102 2.8 26.3 0.5
C6 B:CKM101 3.0 17.1 0.5
CD1 A:ILE84 3.1 25.2 1.0
C4 B:CKM102 3.2 28.8 0.5
C8 B:CKM101 3.3 18.1 0.5
C39 B:CKM102 3.6 37.6 0.5
C16 B:CKM102 3.6 27.2 0.5
C7 B:CKM101 3.6 18.3 0.5
C14 B:CKM102 3.6 22.7 0.5
F37 B:CKM101 3.9 17.2 0.5
N3 B:CKM102 4.0 36.2 0.5
CB A:ALA28 4.0 13.8 1.0
CG2 A:ILE84 4.0 18.5 1.0
CD1 B:ILE50 4.0 29.4 1.0
C15 B:CKM102 4.1 25.6 0.5
CG1 A:ILE84 4.2 16.8 1.0
C2 B:CKM102 4.2 32.5 0.5
OD2 A:ASP25 4.2 28.8 1.0
C38 B:CKM102 4.4 36.8 0.5
CB A:ILE84 4.4 16.3 1.0
S B:CKM101 4.4 16.7 0.5
C1 B:CKM101 4.5 16.0 0.5
CG2 A:VAL32 4.6 20.5 1.0
C B:CKM101 4.6 16.3 0.5
CB B:ILE50 4.6 22.0 1.0
CG1 B:ILE50 4.6 24.0 1.0
O B:CKM101 4.7 16.8 0.5
N19 B:CKM102 4.8 20.0 0.5
CA A:ALA28 4.9 12.6 1.0
C28 B:CKM101 4.9 13.8 0.5
N3 B:CKM101 4.9 14.5 0.5
C27 B:CKM101 4.9 10.7 0.5
C2 B:CKM101 5.0 13.4 0.5
C38 B:CKM101 5.0 15.5 0.5

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: Tue Jul 15 09:54:34 2025

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