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

Enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 (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 (E166V) in Complex with Ensitrelvir (Esv), PDB code: 9cms 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) 28.90 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.195, 101.26, 59.374, 90, 107.74, 90
R / Rfree (%) 15.6 / 19.5

Other elements in 9cms:

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

Chlorine (Cl) 2 atoms

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 (E166V) in Complex with Ensitrelvir (Esv) (pdb code 9cms). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (E166V) in Complex with Ensitrelvir (Esv), PDB code: 9cms:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9cms

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Fluorine binding site 1 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 (E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.9
occ:1.00
F28 A:7YY401 0.0 24.9 1.0
C27 A:7YY401 1.4 23.8 1.0
C29 A:7YY401 2.4 23.5 1.0
C26 A:7YY401 2.4 17.7 1.0
C25 A:7YY401 2.8 20.0 1.0
O A:HOH590 3.1 34.4 1.0
O A:HOH521 3.4 25.4 1.0
CA A:GLN189 3.4 25.5 1.0
CG A:GLN189 3.5 33.6 1.0
CB A:GLN189 3.5 28.1 1.0
O A:HOH544 3.6 21.4 1.0
C30 A:7YY401 3.6 21.6 1.0
C34 A:7YY401 3.6 18.0 1.0
NE2 A:GLN189 3.8 42.4 1.0
O A:ARG188 3.9 25.2 1.0
CD A:GLN189 4.0 38.3 1.0
N A:GLN189 4.0 26.6 1.0
C32 A:7YY401 4.1 18.4 1.0
C A:ARG188 4.1 25.6 1.0
N24 A:7YY401 4.2 19.9 1.0
CB A:MET165 4.5 17.6 1.0
NE2 A:HIS41 4.5 21.8 1.0
C A:GLN189 4.6 30.8 1.0
O36 A:7YY401 4.7 18.9 1.0
F31 A:7YY401 4.7 24.7 1.0
SD A:MET165 4.8 31.2 1.0
OE1 A:GLN189 4.9 36.5 1.0
C35 A:7YY401 5.0 19.0 1.0

Fluorine binding site 2 out of 6 in 9cms

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Fluorine binding site 2 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 (E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.7
occ:1.00
F31 A:7YY401 0.0 24.7 1.0
C30 A:7YY401 1.3 21.6 1.0
C32 A:7YY401 2.4 18.4 1.0
C29 A:7YY401 2.4 23.5 1.0
F33 A:7YY401 2.7 19.4 1.0
CB A:ASP187 3.0 14.7 1.0
CA A:ASP187 3.1 16.8 1.0
C A:ASP187 3.2 23.0 1.0
ND1 A:HIS41 3.6 18.1 1.0
O A:ASP187 3.6 19.3 1.0
C27 A:7YY401 3.6 23.8 1.0
C34 A:7YY401 3.6 18.0 1.0
CG A:HIS41 3.7 18.3 1.0
N A:ARG188 3.7 23.9 1.0
CE1 A:HIS41 3.9 21.8 1.0
CB A:HIS41 4.1 17.9 1.0
CD2 A:HIS41 4.1 22.2 1.0
O A:HOH578 4.1 14.6 1.0
C26 A:7YY401 4.1 17.7 1.0
SD A:MET165 4.2 31.2 1.0
NE2 A:HIS41 4.2 21.8 1.0
CG A:ASP187 4.4 18.8 1.0
CA A:ARG188 4.4 24.7 1.0
ND1 A:HIS164 4.4 14.4 1.0
OH A:TYR54 4.5 20.8 1.0
N A:ASP187 4.5 18.2 1.0
O A:ARG188 4.7 25.2 1.0
C A:ARG188 4.7 25.6 1.0
CB A:HIS164 4.7 17.3 1.0
F28 A:7YY401 4.7 24.9 1.0
OD2 A:ASP187 4.8 15.5 1.0
O A:VAL186 4.9 18.3 1.0
CB A:MET165 4.9 17.6 1.0
CG A:MET165 5.0 24.5 1.0

Fluorine binding site 3 out of 6 in 9cms

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Fluorine binding site 3 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 (E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:19.4
occ:1.00
F33 A:7YY401 0.0 19.4 1.0
C32 A:7YY401 1.3 18.4 1.0
C30 A:7YY401 2.4 21.6 1.0
C34 A:7YY401 2.4 18.0 1.0
F31 A:7YY401 2.7 24.7 1.0
O A:HIS164 3.4 17.0 1.0
CB A:HIS41 3.4 17.9 1.0
SG A:CYS145 3.5 17.2 1.0
CG A:HIS41 3.5 18.3 1.0
C29 A:7YY401 3.6 23.5 1.0
CD2 A:HIS41 3.6 22.2 1.0
C26 A:7YY401 3.6 17.7 1.0
CB A:HIS164 3.8 17.3 1.0
ND1 A:HIS164 3.8 14.4 1.0
C A:HIS164 3.9 15.8 1.0
CA A:HIS164 4.0 15.8 1.0
C27 A:7YY401 4.1 23.8 1.0
O A:HOH578 4.1 14.6 1.0
CG A:HIS164 4.2 15.4 1.0
ND1 A:HIS41 4.4 18.1 1.0
CL2 A:7YY401 4.4 19.4 1.0
NE2 A:HIS41 4.5 21.8 1.0
CB A:PRO39 4.7 13.1 1.0
CB A:MET165 4.8 17.6 1.0
N A:MET165 4.9 12.5 1.0
CE1 A:HIS41 4.9 21.8 1.0
CA A:HIS41 4.9 17.8 1.0
C25 A:7YY401 4.9 20.0 1.0
CE1 A:HIS164 5.0 14.1 1.0

Fluorine binding site 4 out of 6 in 9cms

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Fluorine binding site 4 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 4 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:25.6
occ:1.00
F28 B:7YY401 0.0 25.6 1.0
C27 B:7YY401 1.4 24.4 1.0
C26 B:7YY401 2.4 17.0 1.0
C29 B:7YY401 2.4 25.2 1.0
C25 B:7YY401 2.8 18.9 1.0
CG B:GLN189 3.3 38.1 1.0
CA B:GLN189 3.3 30.7 1.0
O B:HOH524 3.4 30.3 1.0
CB B:GLN189 3.4 35.3 1.0
O B:HOH592 3.4 35.1 1.0
O B:HOH555 3.6 25.1 1.0
C30 B:7YY401 3.6 23.3 1.0
C34 B:7YY401 3.6 16.6 1.0
N B:GLN189 3.8 30.8 1.0
O B:ARG188 3.8 29.3 1.0
C B:ARG188 4.0 32.1 1.0
C32 B:7YY401 4.1 22.2 1.0
N24 B:7YY401 4.2 21.6 1.0
OE1 B:GLN189 4.3 50.9 1.0
CD B:GLN189 4.3 46.2 1.0
CB B:MET165 4.5 21.1 1.0
NE2 B:HIS41 4.5 24.4 1.0
C B:GLN189 4.6 37.3 1.0
O36 B:7YY401 4.6 21.5 1.0
F31 B:7YY401 4.7 27.9 1.0
CE1 B:HIS41 4.9 21.6 1.0
C35 B:7YY401 4.9 19.6 1.0
SD B:MET165 4.9 30.0 1.0
N12 B:7YY401 5.0 23.4 1.0

Fluorine binding site 5 out of 6 in 9cms

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Fluorine binding site 5 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 5 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:27.9
occ:1.00
F31 B:7YY401 0.0 27.9 1.0
C30 B:7YY401 1.3 23.3 1.0
C32 B:7YY401 2.3 22.2 1.0
C29 B:7YY401 2.4 25.2 1.0
F33 B:7YY401 2.7 22.1 1.0
CB B:ASP187 2.9 20.9 1.0
CA B:ASP187 3.0 23.2 1.0
C B:ASP187 3.2 24.7 1.0
O B:ASP187 3.5 22.9 1.0
ND1 B:HIS41 3.6 19.5 1.0
C27 B:7YY401 3.6 24.4 1.0
C34 B:7YY401 3.6 16.6 1.0
CG B:HIS41 3.7 20.9 1.0
N B:ARG188 3.8 24.8 1.0
CE1 B:HIS41 4.0 21.6 1.0
CB B:HIS41 4.1 18.8 1.0
C26 B:7YY401 4.1 17.0 1.0
O B:HOH544 4.2 20.0 1.0
SD B:MET165 4.2 30.0 1.0
CD2 B:HIS41 4.2 20.3 1.0
CG B:ASP187 4.2 22.8 1.0
NE2 B:HIS41 4.3 24.4 1.0
N B:ASP187 4.5 20.9 1.0
CA B:ARG188 4.5 28.8 1.0
OH B:TYR54 4.5 23.1 1.0
CD2 B:HIS164 4.5 16.7 1.0
OD2 B:ASP187 4.7 17.4 1.0
C B:ARG188 4.7 32.1 1.0
F28 B:7YY401 4.7 25.6 1.0
O B:ARG188 4.7 29.3 1.0
CB B:HIS164 4.8 17.3 1.0
CB B:MET165 4.8 21.1 1.0
O B:VAL186 4.9 25.2 1.0
CG B:MET165 5.0 20.0 1.0

Fluorine binding site 6 out of 6 in 9cms

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Fluorine binding site 6 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (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 6 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Drug Resistant Mutant (E166V) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:22.1
occ:1.00
F33 B:7YY401 0.0 22.1 1.0
C32 B:7YY401 1.4 22.2 1.0
C30 B:7YY401 2.4 23.3 1.0
C34 B:7YY401 2.4 16.6 1.0
F31 B:7YY401 2.7 27.9 1.0
O B:HIS164 3.4 18.6 1.0
CB B:HIS41 3.5 18.8 1.0
SG B:CYS145 3.5 18.1 1.0
CG B:HIS41 3.6 20.9 1.0
C29 B:7YY401 3.6 25.2 1.0
C26 B:7YY401 3.6 17.0 1.0
CD2 B:HIS41 3.7 20.3 1.0
C B:HIS164 3.8 20.0 1.0
CB B:HIS164 3.9 17.3 1.0
CD2 B:HIS164 3.9 16.7 1.0
CA B:HIS164 4.0 16.9 1.0
C27 B:7YY401 4.1 24.4 1.0
O B:HOH544 4.2 20.0 1.0
CG B:HIS164 4.2 20.0 1.0
ND1 B:HIS41 4.3 19.5 1.0
CL2 B:7YY401 4.4 19.9 1.0
NE2 B:HIS41 4.5 24.4 1.0
CB B:PRO39 4.7 16.5 1.0
N B:MET165 4.8 16.8 1.0
CB B:MET165 4.8 21.1 1.0
CE1 B:HIS41 4.8 21.6 1.0
CA B:HIS41 4.9 18.2 1.0
CB B:ASP187 4.9 20.9 1.0
C25 B:7YY401 4.9 18.9 1.0
CB B:CYS145 4.9 16.2 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 20:07:50 2024

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