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Zinc in PDB 4tyd: Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease

Protein crystallography data

The structure of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease, PDB code: 4tyd was solved by C.Parsy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 140.691, 143.197, 240.550, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.7

Other elements in 4tyd:

The structure of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease (pdb code 4tyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease, PDB code: 4tyd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4tyd

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Zinc binding site 1 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:80.9
occ:1.00
SG A:CYS97 2.1 72.0 1.0
SG A:CYS145 2.2 74.4 1.0
SG A:CYS99 2.4 77.3 1.0
CB A:CYS145 3.1 70.8 1.0
CB A:CYS97 3.2 70.3 1.0
CB A:CYS99 3.6 82.2 1.0
ND1 A:HIS149 3.7 79.0 1.0
N A:CYS99 3.7 82.0 1.0
CA A:CYS97 3.8 72.9 1.0
N A:THR98 3.9 79.4 1.0
CB A:HIS149 4.1 72.9 1.0
CA A:CYS99 4.2 83.1 1.0
C A:CYS97 4.3 76.3 1.0
CG A:HIS149 4.3 76.2 1.0
CB A:SER147 4.5 78.9 1.0
CA A:CYS145 4.6 68.3 1.0
OG A:SER147 4.6 80.7 1.0
CE1 A:HIS149 4.7 82.0 1.0
C A:THR98 4.8 84.1 1.0
C A:CYS99 4.8 82.0 1.0
N A:GLY100 4.9 80.2 1.0
CA A:THR98 4.9 83.2 1.0
N A:SER147 5.0 74.2 1.0

Zinc binding site 2 out of 12 in 4tyd

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Zinc binding site 2 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:77.2
occ:1.00
SG B:CYS97 2.0 68.8 1.0
SG B:CYS99 2.4 77.4 1.0
SG B:CYS145 2.5 66.6 1.0
CB B:CYS97 3.3 66.3 1.0
CB B:CYS145 3.3 65.7 1.0
N B:CYS99 3.4 80.3 1.0
ND1 B:HIS149 3.5 76.8 1.0
CB B:CYS99 3.6 82.1 1.0
N B:THR98 3.6 75.4 1.0
CA B:CYS97 3.7 68.7 1.0
C B:CYS97 4.0 72.3 1.0
CB B:HIS149 4.1 68.6 1.0
CA B:CYS99 4.1 83.0 1.0
CG B:HIS149 4.2 72.2 1.0
C B:THR98 4.5 81.7 1.0
CE1 B:HIS149 4.5 80.0 1.0
CB B:SER147 4.6 75.5 1.0
CA B:THR98 4.6 79.9 1.0
CA B:CYS145 4.8 63.4 1.0
C B:CYS99 4.8 82.9 1.0
N B:GLY100 4.8 80.7 1.0

Zinc binding site 3 out of 12 in 4tyd

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Zinc binding site 3 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:86.5
occ:1.00
SG C:CYS97 2.3 78.5 1.0
SG C:CYS145 2.3 71.1 1.0
SG C:CYS99 2.4 85.0 1.0
CB C:CYS145 3.0 71.5 1.0
CB C:CYS97 3.3 75.9 1.0
CB C:CYS99 3.7 89.1 1.0
N C:CYS99 3.8 88.7 1.0
CA C:CYS97 3.8 78.6 1.0
N C:THR98 3.8 85.0 1.0
ND1 C:HIS149 3.8 79.8 1.0
CB C:HIS149 4.1 74.6 1.0
C C:CYS97 4.3 82.0 1.0
CA C:CYS99 4.3 90.5 1.0
CG C:HIS149 4.5 77.1 1.0
CA C:CYS145 4.5 68.8 1.0
CB C:SER147 4.6 79.3 1.0
OG C:SER147 4.7 81.0 1.0
C C:THR98 4.8 90.7 1.0
CA C:THR98 4.9 89.0 1.0
CE1 C:HIS149 4.9 82.7 1.0

Zinc binding site 4 out of 12 in 4tyd

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Zinc binding site 4 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:94.3
occ:1.00
SG D:CYS97 2.3 78.7 1.0
SG D:CYS145 2.5 78.8 1.0
SG D:CYS99 2.8 85.2 1.0
CB D:CYS97 3.4 77.2 1.0
N D:THR98 3.4 86.5 1.0
N D:CYS99 3.5 89.6 1.0
CB D:CYS99 3.5 90.5 1.0
ND1 D:HIS149 3.5 86.6 1.0
CA D:CYS97 3.5 80.2 1.0
CB D:CYS145 3.7 76.8 1.0
CB D:HIS149 3.9 78.9 1.0
C D:CYS97 3.9 83.6 1.0
CG D:HIS149 4.1 83.0 1.0
CA D:CYS99 4.1 91.8 1.0
C D:THR98 4.4 92.0 1.0
CA D:THR98 4.5 90.2 1.0
CE1 D:HIS149 4.5 89.7 1.0
CB D:SER147 4.5 86.3 1.0
OG D:SER147 4.8 89.8 1.0
N D:CYS97 4.9 78.8 1.0
N D:GLY100 4.9 88.0 1.0
C D:CYS99 5.0 91.2 1.0

Zinc binding site 5 out of 12 in 4tyd

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Zinc binding site 5 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:53.8
occ:1.00
SG E:CYS99 2.0 60.0 1.0
SG E:CYS97 2.2 56.6 1.0
SG E:CYS145 2.3 51.4 1.0
CB E:CYS145 3.2 51.6 1.0
CB E:CYS99 3.3 62.7 1.0
CB E:CYS97 3.4 57.3 1.0
N E:CYS99 3.6 64.7 1.0
ND1 E:HIS149 3.8 59.2 1.0
CA E:CYS97 3.8 60.1 1.0
N E:THR98 3.9 64.7 1.0
CB E:HIS149 3.9 54.5 1.0
CA E:CYS99 4.0 64.7 1.0
CG E:HIS149 4.2 57.0 1.0
C E:CYS97 4.3 63.1 1.0
CB E:SER147 4.6 56.1 1.0
CA E:CYS145 4.6 49.7 1.0
C E:THR98 4.7 67.4 1.0
OG E:SER147 4.7 57.9 1.0
C E:CYS99 4.8 64.4 1.0
CE1 E:HIS149 4.8 60.5 1.0
CA E:THR98 4.9 67.5 1.0
N E:GLY100 5.0 63.8 1.0

Zinc binding site 6 out of 12 in 4tyd

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Zinc binding site 6 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:96.0
occ:1.00
SG F:CYS97 1.7 92.7 1.0
SG F:CYS145 2.6 88.6 1.0
SG F:CYS99 2.6 98.7 1.0
CB F:CYS97 3.2 89.3 1.0
CB F:CYS99 3.3 0.6 1.0
N F:CYS99 3.4 0.9 1.0
CB F:CYS145 3.5 85.8 1.0
N F:THR98 3.6 0.3 1.0
ND1 F:HIS149 3.6 96.2 1.0
CA F:CYS97 3.7 92.3 1.0
CA F:CYS99 3.9 0.1 1.0
C F:CYS97 4.1 96.3 1.0
CB F:HIS149 4.1 88.2 1.0
CG F:HIS149 4.3 91.7 1.0
C F:THR98 4.5 0.0 1.0
CA F:THR98 4.6 0.8 1.0
CB F:SER147 4.6 96.3 1.0
N F:GLY100 4.7 0.6 1.0
CE1 F:HIS149 4.7 99.0 1.0
OG F:SER147 4.7 0.8 1.0
C F:CYS99 4.7 0.3 1.0
CA F:CYS145 5.0 82.5 1.0

Zinc binding site 7 out of 12 in 4tyd

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Zinc binding site 7 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:85.4
occ:1.00
SG G:CYS97 2.2 86.5 1.0
SG G:CYS99 2.4 97.6 1.0
SG G:CYS145 2.7 85.6 1.0
CB G:CYS145 3.3 82.4 1.0
CB G:CYS97 3.4 83.2 1.0
CB G:CYS99 3.4 0.9 1.0
N G:CYS99 3.5 0.5 1.0
CA G:CYS97 3.7 86.8 1.0
N G:THR98 3.7 96.6 1.0
CA G:CYS99 4.0 0.5 1.0
C G:CYS97 4.1 91.4 1.0
ND1 G:HIS149 4.1 94.8 1.0
CB G:HIS149 4.3 84.8 1.0
C G:THR98 4.6 0.8 1.0
CG G:HIS149 4.6 89.7 1.0
C G:CYS99 4.7 0.6 1.0
CA G:THR98 4.7 1.0 1.0
CA G:CYS145 4.8 79.0 1.0
CB G:SER147 4.9 97.3 1.0
N G:GLY100 4.9 99.7 1.0
OG G:SER147 4.9 0.5 1.0

Zinc binding site 8 out of 12 in 4tyd

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Zinc binding site 8 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:0.0
occ:1.00
SG H:CYS97 1.9 0.6 1.0
SG H:CYS145 2.6 0.2 1.0
SG H:CYS99 2.7 0.5 1.0
CB H:CYS145 3.2 0.5 1.0
CB H:CYS97 3.2 0.7 1.0
N H:CYS99 3.6 0.2 1.0
CB H:CYS99 3.7 0.4 1.0
N H:THR98 3.7 0.7 1.0
CA H:CYS97 3.8 0.7 1.0
ND1 H:HIS149 3.9 0.0 1.0
C H:CYS97 4.2 0.0 1.0
CA H:CYS99 4.2 0.8 1.0
CB H:HIS149 4.3 0.3 1.0
OG H:SER147 4.5 0.5 1.0
CG H:HIS149 4.6 0.5 1.0
C H:THR98 4.6 0.8 1.0
N H:GLY100 4.7 0.7 1.0
CA H:THR98 4.7 0.8 1.0
CA H:CYS145 4.7 98.0 1.0
CB H:SER147 4.7 0.5 1.0
C H:CYS99 4.9 0.8 1.0
CE1 H:HIS149 5.0 1.0 1.0

Zinc binding site 9 out of 12 in 4tyd

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Zinc binding site 9 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:92.1
occ:1.00
SG J:CYS97 1.9 80.1 1.0
SG J:CYS145 2.5 75.0 1.0
SG J:CYS99 2.7 85.2 1.0
CB J:CYS97 3.2 78.0 1.0
ND1 J:HIS149 3.4 83.9 1.0
N J:THR98 3.5 85.6 1.0
CB J:CYS145 3.5 76.0 1.0
CA J:CYS97 3.5 79.8 1.0
N J:CYS99 3.5 89.3 1.0
CB J:HIS149 3.7 76.7 1.0
CB J:CYS99 3.7 89.5 1.0
C J:CYS97 3.9 83.3 1.0
CG J:HIS149 4.0 80.2 1.0
CA J:CYS99 4.2 91.2 1.0
C J:THR98 4.5 91.3 1.0
CE1 J:HIS149 4.5 86.0 1.0
CA J:THR98 4.5 89.6 1.0
CB J:SER147 4.7 80.7 1.0
N J:CYS97 4.8 78.5 1.0
CA J:HIS149 4.8 73.3 1.0
N J:GLY100 4.8 89.6 1.0
CA J:CYS145 4.9 73.7 1.0
N J:HIS149 4.9 73.0 1.0
C J:CYS99 5.0 91.5 1.0

Zinc binding site 10 out of 12 in 4tyd

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Zinc binding site 10 out of 12 in the Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:0.2
occ:1.00
SG K:CYS97 2.2 0.4 1.0
SG K:CYS145 2.6 0.5 1.0
SG K:CYS99 3.1 0.2 1.0
CB K:CYS145 3.4 0.9 1.0
CB K:CYS97 3.4 0.8 1.0
N K:CYS99 3.7 0.8 1.0
CB K:CYS99 3.7 0.5 1.0
ND1 K:HIS149 3.7 0.7 1.0
N K:THR98 3.8 0.2 1.0
CA K:CYS97 3.9 0.7 1.0
CB K:HIS149 4.0 0.1 1.0
OG K:SER147 4.2 0.7 1.0
C K:CYS97 4.3 0.7 1.0
CB K:SER147 4.3 0.9 1.0
CG K:HIS149 4.3 0.8 1.0
CA K:CYS99 4.3 0.1 1.0
C K:THR98 4.7 0.6 1.0
CE1 K:HIS149 4.8 0.2 1.0
CA K:THR98 4.8 0.1 1.0
CA K:CYS145 4.9 0.4 1.0
N K:GLY100 4.9 0.8 1.0

Reference:

C.Parsy, F.R.Alexandre, G.Brandt, C.Caillet, S.Cappelle, D.Chaves, T.Convard, M.Derock, D.Gloux, Y.Griffon, L.Lallos, F.Leroy, M.Liuzzi, A.G.Loi, L.Moulat, C.Musiu, H.Rahali, V.Roques, M.Seifer, D.Standring, D.Surleraux. Structure-Based Design of A Novel Series of Azetidine Inhibitors of the Hepatitis C Virus NS3/4A Serine Protease. Bioorg.Med.Chem.Lett. V. 24 4444 2014.
ISSN: ESSN 1464-3405
PubMed: 25155387
DOI: 10.1016/J.BMCL.2014.08.002
Page generated: Wed Dec 16 05:47:29 2020

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