Fluorine in PDB 9cmu: Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv)

Enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv)

All present enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv):
3.4.22.69;

Protein crystallography data

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv), PDB code: 9cmu was solved by A.Kovalevsky, L.Coates, O.Gerlits, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.35 / 2.00
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.039, 83.007, 90.866, 90, 95.29, 90
R / Rfree (%) 15.9 / 20.2

Other elements in 9cmu:

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv) (pdb code 9cmu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv), PDB code: 9cmu:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 9cmu

Go back to Fluorine Binding Sites List in 9cmu
Fluorine binding site 1 out of 3 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.6
occ:1.00
 F28 A:7YY401 0.0 39.6 1.0
C27 A:7YY401 1.4 28.4 1.0
C29 A:7YY401 2.4 30.6 1.0
C26 A:7YY401 2.4 29.9 1.0
C25 A:7YY401 2.8 35.0 1.0
O A:HOH520 3.1 39.0 1.0
CA A:GLN189 3.2 41.9 1.0
CB A:GLN189 3.3 41.3 1.0
O A:HOH576 3.3 48.7 1.0
CG A:GLN189 3.3 37.8 1.0
C30 A:7YY401 3.6 33.9 1.0
C34 A:7YY401 3.6 31.2 1.0
O A:HOH532 3.7 41.5 1.0
N A:GLN189 3.8 41.7 1.0
O A:ARG188 4.0 34.6 1.0
NE2 A:GLN189 4.1 59.9 1.0
C A:ARG188 4.1 42.2 1.0
C32 A:7YY401 4.1 30.9 1.0
CD A:GLN189 4.1 51.2 1.0
N24 A:7YY401 4.2 37.2 1.0
CB A:MET165 4.4 31.4 1.0
C A:GLN189 4.5 48.0 1.0
O36 A:7YY401 4.6 36.1 1.0
NE2 A:HIS41 4.6 37.3 1.0
F31 A:7YY401 4.7 41.1 1.0
SD A:MET165 4.8 48.3 1.0
N A:THR190 4.9 45.4 1.0
C35 A:7YY401 4.9 31.5 1.0

Fluorine binding site 2 out of 3 in 9cmu

Go back to Fluorine Binding Sites List in 9cmu
Fluorine binding site 2 out of 3 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.1
occ:1.00
 F31 A:7YY401 0.0 41.1 1.0
C30 A:7YY401 1.3 33.9 1.0
C32 A:7YY401 2.3 30.9 1.0
C29 A:7YY401 2.4 30.6 1.0
F33 A:7YY401 2.7 37.8 1.0
CB A:ASP187 3.0 31.3 1.0
CA A:ASP187 3.1 36.9 1.0
C A:ASP187 3.2 40.3 1.0
ND1 A:HIS41 3.5 33.0 1.0
O A:ASP187 3.5 35.3 1.0
C27 A:7YY401 3.6 28.4 1.0
C34 A:7YY401 3.6 31.2 1.0
CG A:HIS41 3.7 36.1 1.0
N A:ARG188 3.7 34.2 1.0
CE1 A:HIS41 3.9 35.5 1.0
CB A:HIS41 4.0 29.1 1.0
CD2 A:HIS41 4.1 31.2 1.0
C26 A:7YY401 4.1 29.9 1.0
O A:HOH555 4.1 32.5 1.0
SD A:MET165 4.2 48.3 1.0
NE2 A:HIS41 4.2 37.3 1.0
CA A:ARG188 4.3 41.6 1.0
CG A:ASP187 4.4 35.1 1.0
OH A:TYR54 4.4 40.3 1.0
N A:ASP187 4.5 36.6 1.0
ND1 A:HIS164 4.5 30.9 1.0
CB A:HIS164 4.7 23.8 1.0
C A:ARG188 4.7 42.2 1.0
F28 A:7YY401 4.7 39.6 1.0
CB A:MET165 4.8 31.4 1.0
OD2 A:ASP187 4.9 37.8 1.0
O A:ARG188 4.9 34.6 1.0
O A:VAL186 4.9 35.7 1.0

Fluorine binding site 3 out of 3 in 9cmu

Go back to Fluorine Binding Sites List in 9cmu
Fluorine binding site 3 out of 3 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (L50F, E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:37.8
occ:1.00
 F33 A:7YY401 0.0 37.8 1.0
C32 A:7YY401 1.3 30.9 1.0
C30 A:7YY401 2.4 33.9 1.0
C34 A:7YY401 2.4 31.2 1.0
F31 A:7YY401 2.7 41.1 1.0
O A:HIS164 3.4 34.4 1.0
SG A:CYS145 3.4 33.9 1.0
CB A:HIS41 3.4 29.1 1.0
CG A:HIS41 3.6 36.1 1.0
C29 A:7YY401 3.6 30.6 1.0
C26 A:7YY401 3.6 29.9 1.0
CD2 A:HIS41 3.7 31.2 1.0
CB A:HIS164 3.9 23.8 1.0
C A:HIS164 3.9 31.5 1.0
CA A:HIS164 4.0 30.8 1.0
ND1 A:HIS164 4.0 30.9 1.0
C27 A:7YY401 4.1 28.4 1.0
O A:HOH555 4.1 32.5 1.0
CL2 A:7YY401 4.3 38.9 1.0
CG A:HIS164 4.3 29.2 1.0
ND1 A:HIS41 4.3 33.0 1.0
NE2 A:HIS41 4.5 37.3 1.0
CB A:PRO39 4.7 29.4 1.0
CB A:MET165 4.8 31.4 1.0
N A:MET165 4.8 28.2 1.0
CA A:HIS41 4.9 43.1 1.0
CE1 A:HIS41 4.9 35.5 1.0
C25 A:7YY401 4.9 35.0 1.0
CB A:CYS145 4.9 25.5 1.0
CB A:ASP187 5.0 31.3 1.0

Reference:

A.Kovalevsky, A.Aniana, R.Ghirlando, L.Coates, V.N.Drago, L.Wear, O.Gerlits, N.T.Nashed, J.M.Louis. Effects of Sars-Cov-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 39370853
DOI: 10.1021/ACS.JMEDCHEM.4C01781
Page generated: Thu Oct 31 20:07:49 2024

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