Chlorine in PDB 7q5f: Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

Enzymatic activity of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 7q5f was solved by E.Costanzi, N.Demitri, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.43 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.866, 100.441, 103.631, 90, 90, 90
R / Rfree (%) 17.2 / 19.6

Other elements in 7q5f:

The structure of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 7q5f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 7q5f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7q5f

Go back to Chlorine Binding Sites List in 7q5f
Chlorine binding site 1 out of 6 in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:111.0
occ:1.00
 CL A:90X401 0.0 111.0 1.0
C5 A:90X401 1.8 68.8 1.0
C6 A:90X401 2.8 53.2 1.0
C4 A:90X401 2.8 53.8 1.0
H6 A:90X401 2.9 63.8 1.0
H41 A:90X401 2.9 64.6 1.0
H2C A:90X401 3.5 44.7 1.0
H2B A:90X401 3.6 44.7 1.0
O A:HOH694 3.8 37.1 1.0
HB2 A:ASN142 3.9 37.8 1.0
H2A A:90X401 3.9 37.4 1.0
C17 A:90X401 4.0 37.2 1.0
C7 A:90X401 4.1 49.8 1.0
C3 A:90X401 4.1 57.2 1.0
C16 A:90X401 4.3 31.1 1.0
H19 A:90X401 4.4 37.4 1.0
C2 A:90X401 4.6 54.6 1.0
O B:HOH581 4.6 35.8 1.0
CB A:ASN142 4.8 31.5 1.0
H31 A:90X401 4.9 68.6 1.0
H A:ASN142 5.0 34.1 1.0

Chlorine binding site 2 out of 6 in 7q5f

Go back to Chlorine Binding Sites List in 7q5f
Chlorine binding site 2 out of 6 in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:81.3
occ:1.00
 CL1 A:90X401 0.0 81.3 1.0
C7 A:90X401 1.8 49.8 1.0
C2 A:90X401 2.7 54.6 1.0
C6 A:90X401 2.8 53.2 1.0
O A:HOH591 2.8 43.5 1.0
O1 A:90X401 2.9 49.5 1.0
H6 A:90X401 2.9 63.8 1.0
HG2 A:GLU166 3.1 34.9 1.0
HB3 A:GLU166 3.1 30.1 1.0
OE2 A:GLU166 3.6 32.6 1.0
CG A:GLU166 3.7 29.1 1.0
O A:GLU166 3.7 25.8 1.0
CB A:GLU166 3.8 25.1 1.0
CD A:GLU166 3.9 32.8 1.0
C3 A:90X401 4.0 57.2 1.0
C5 A:90X401 4.1 68.8 1.0
O A:LEU167 4.1 29.2 1.0
C A:GLU166 4.2 26.8 1.0
H2C A:90X401 4.3 44.7 1.0
C1 A:90X401 4.3 43.0 1.0
HA A:PRO168 4.3 31.3 1.0
HB2 A:GLU166 4.5 30.1 1.0
HG3 A:GLU166 4.6 34.9 1.0
C4 A:90X401 4.6 53.8 1.0
C A:LEU167 4.6 33.1 1.0
H11 A:90X401 4.6 51.6 1.0
CA A:GLU166 4.6 25.8 1.0
O A:90X401 4.8 31.9 1.0
N A:LEU167 4.9 23.6 1.0
H31 A:90X401 4.9 68.6 1.0
H12 A:90X401 4.9 51.6 1.0
OE1 A:GLU166 5.0 27.6 1.0
H A:GLU166 5.0 26.2 1.0

Chlorine binding site 3 out of 6 in 7q5f

Go back to Chlorine Binding Sites List in 7q5f
Chlorine binding site 3 out of 6 in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:41.1
occ:1.00
 H B:ALA285 2.5 32.9 1.0
H A:ALA285 2.5 31.0 1.0
HB3 A:ALA285 3.2 33.9 1.0
H A:LEU286 3.3 29.9 1.0
H B:LEU286 3.3 28.1 1.0
N B:ALA285 3.3 27.4 1.0
HG B:LEU286 3.3 39.6 1.0
N A:ALA285 3.3 25.9 1.0
HA B:SER284 3.4 29.7 1.0
HB3 B:ALA285 3.4 34.9 1.0
HG A:LEU286 3.4 44.6 1.0
OG B:SER284 3.5 36.7 1.0
OG A:SER284 3.5 38.1 1.0
HD12 A:LEU286 3.6 42.3 1.0
HA A:SER284 3.6 31.4 1.0
HB2 A:LEU286 3.6 33.0 1.0
HD12 B:LEU286 3.7 39.8 1.0
N A:LEU286 3.7 24.9 1.0
N B:LEU286 3.9 23.4 1.0
CB A:ALA285 4.0 28.2 1.0
CA A:ALA285 4.0 26.2 1.0
HG A:SER284 4.0 45.7 1.0
HB2 B:LEU286 4.0 34.8 1.0
CG A:LEU286 4.0 37.2 1.0
HG B:SER284 4.0 44.0 1.0
CA B:SER284 4.1 24.8 1.0
CG B:LEU286 4.1 33.0 1.0
CA B:ALA285 4.1 26.1 1.0
CB B:ALA285 4.1 29.1 1.0
C A:ALA285 4.1 27.0 1.0
C B:SER284 4.2 25.7 1.0
CB A:LEU286 4.2 27.5 1.0
CD1 A:LEU286 4.2 35.2 1.0
CA A:SER284 4.2 26.1 1.0
CD1 B:LEU286 4.3 33.1 1.0
C A:SER284 4.3 25.6 1.0
CB B:SER284 4.3 26.0 1.0
C B:ALA285 4.3 28.1 1.0
HB2 A:ALA285 4.4 33.9 1.0
HD11 B:LEU286 4.4 39.8 1.0
CB A:SER284 4.4 26.8 1.0
HB2 B:ALA285 4.4 34.9 1.0
CB B:LEU286 4.5 29.0 1.0
HD11 A:LEU286 4.5 42.3 1.0
HB2 B:SER284 4.6 31.2 1.0
CA A:LEU286 4.6 23.1 1.0
HB2 A:SER284 4.7 32.2 1.0
HB1 A:ALA285 4.7 33.9 1.0
CA B:LEU286 4.8 24.0 1.0
HB1 B:ALA285 4.9 34.9 1.0
HA A:ALA285 4.9 31.4 1.0
HA B:ALA285 5.0 31.3 1.0

Chlorine binding site 4 out of 6 in 7q5f

Go back to Chlorine Binding Sites List in 7q5f
Chlorine binding site 4 out of 6 in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:21.7
occ:1.00
 HE21 A:GLN110 2.4 25.7 1.0
H A:GLN107 2.5 21.3 1.0
O A:HOH740 3.0 30.4 1.0
HA A:ILE106 3.1 24.5 1.0
HB2 A:GLN110 3.2 22.0 1.0
HB2 A:GLN107 3.2 27.3 1.0
NE2 A:GLN110 3.3 21.4 1.0
N A:GLN107 3.3 17.7 1.0
HG2 A:GLN110 3.4 24.3 1.0
HB A:ILE106 3.4 19.4 1.0
HG2 A:GLN107 3.5 34.2 1.0
HG22 A:ILE106 3.6 24.9 1.0
HE22 A:GLN110 3.8 25.7 1.0
CA A:ILE106 3.8 20.4 1.0
CB A:GLN110 3.9 18.3 1.0
CG A:GLN110 3.9 20.3 1.0
CB A:GLN107 3.9 22.7 1.0
CB A:ILE106 3.9 16.2 1.0
C A:ILE106 4.1 23.5 1.0
CD A:GLN110 4.1 22.1 1.0
CG A:GLN107 4.1 28.5 1.0
HB3 A:GLN110 4.1 22.0 1.0
CA A:GLN107 4.2 19.7 1.0
CG2 A:ILE106 4.2 20.8 1.0
HG3 A:GLN107 4.3 34.2 1.0
O A:GLN107 4.6 18.4 1.0
HG21 A:ILE106 4.6 24.9 1.0
HB3 A:GLN107 4.8 27.3 1.0
HG3 A:GLN110 4.8 24.3 1.0
C A:GLN107 4.9 19.2 1.0
HG23 A:ILE106 5.0 24.9 1.0
O A:ARG105 5.0 21.9 1.0

Chlorine binding site 5 out of 6 in 7q5f

Go back to Chlorine Binding Sites List in 7q5f
Chlorine binding site 5 out of 6 in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:75.4
occ:1.00
 CL B:90X401 0.0 75.4 1.0
C5 B:90X401 1.8 59.8 1.0
C6 B:90X401 2.7 51.7 1.0
H6 B:90X401 2.8 62.0 1.0
C4 B:90X401 2.8 53.3 1.0
H41 B:90X401 3.0 64.0 1.0
H2C B:90X401 3.4 34.5 1.0
H2B B:90X401 3.7 34.5 1.0
O A:HOH730 3.9 38.1 1.0
C7 B:90X401 3.9 48.5 1.0
C17 B:90X401 4.0 28.8 1.0
C3 B:90X401 4.1 41.2 1.0
O B:HOH637 4.2 34.5 1.0
H2A B:90X401 4.2 33.5 1.0
C2 B:90X401 4.5 46.0 1.0
C16 B:90X401 4.6 28.0 1.0
HB2 B:ASN142 4.6 42.5 1.0
H19 B:90X401 4.8 33.5 1.0
H31 B:90X401 5.0 49.5 1.0

Chlorine binding site 6 out of 6 in 7q5f

Go back to Chlorine Binding Sites List in 7q5f
Chlorine binding site 6 out of 6 in the Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of F2F-2020216-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:70.0
occ:1.00
 CL1 B:90X401 0.0 70.0 1.0
C7 B:90X401 1.7 48.5 1.0
C2 B:90X401 2.6 46.0 1.0
C6 B:90X401 2.7 51.7 1.0
O1 B:90X401 2.7 37.9 1.0
H6 B:90X401 2.8 62.0 1.0
O B:HOH555 2.9 42.7 1.0
HG2 B:GLU166 3.0 29.7 1.0
HB3 B:GLU166 3.4 27.3 1.0
O B:GLU166 3.7 28.3 1.0
CG B:GLU166 3.7 24.8 1.0
OE2 B:GLU166 3.7 33.8 1.0
C3 B:90X401 3.9 41.2 1.0
C5 B:90X401 3.9 59.8 1.0
HA B:PRO168 3.9 39.0 1.0
CB B:GLU166 4.0 22.8 1.0
C B:GLU166 4.0 28.1 1.0
CD B:GLU166 4.0 35.1 1.0
C1 B:90X401 4.1 35.8 1.0
O B:LEU167 4.1 26.5 1.0
C B:LEU167 4.3 30.4 1.0
H11 B:90X401 4.3 43.0 1.0
C4 B:90X401 4.4 53.3 1.0
N B:LEU167 4.5 22.8 1.0
HG3 B:GLU166 4.5 29.7 1.0
H2C B:90X401 4.6 34.5 1.0
H12 B:90X401 4.6 43.0 1.0
CA B:GLU166 4.6 20.5 1.0
HA B:LEU167 4.7 29.3 1.0
N B:PRO168 4.7 29.7 1.0
CA B:PRO168 4.7 32.5 1.0
CA B:LEU167 4.7 24.4 1.0
HB2 B:GLU166 4.8 27.3 1.0
H31 B:90X401 4.8 49.5 1.0
O B:90X401 4.8 25.9 1.0
H B:GLU166 4.9 23.7 1.0
C B:90X401 4.9 37.1 1.0

Reference:

S.Pelliccia, C.Cerchia, F.Esposito, R.Cannalire, A.Corona, E.Costanzi, M.Kuzikov, P.Gribbon, A.Zaliani, M.Brindisi, P.Storici, E.Tramontano, V.Summa. Easy Access to Alpha-Ketoamides As Sars-Cov-2 and Mers M Pro Inhibitors Via the Padam Oxidation Route. Eur.J.Med.Chem. V. 244 14853 2022.
ISSN: ISSN 0223-5234
PubMed: 36332546
DOI: 10.1016/J.EJMECH.2022.114853
Page generated: Tue Jul 30 03:03:30 2024

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