Atomistry » Fluorine » PDB 9cdm-9f2h » 9cms
Atomistry »
  Fluorine »
    PDB 9cdm-9f2h »
      9cms »

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

Go back to Fluorine Binding Sites List in 9cms
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

Go back to Fluorine Binding Sites List in 9cms
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

Go back to Fluorine Binding Sites List in 9cms
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

Go back to Fluorine Binding Sites List in 9cms
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

Go back to Fluorine Binding Sites List in 9cms
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

Go back to Fluorine Binding Sites List in 9cms
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: Wed Jul 16 10:43:33 2025

Last articles

Fe in 6XAK
Fe in 6XCX
Fe in 6XAJ
Fe in 6XAM
Fe in 6XAL
Fe in 6X5K
Fe in 6X6U
Fe in 6X1O
Fe in 6XAI
Fe in 6XA3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy