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Fluorine in PDB 5w26: Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

Enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

All present enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid:
3.2.1.18;

Protein crystallography data

The structure of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w26 was solved by V.A.Streltsov, J.Mckimm-Breschkin, S.Barrett, P.Pilling, S.Hader, A.G.Watt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.00 / 1.90
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.940, 180.940, 180.940, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.7

Other elements in 5w26:

The structure of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid (pdb code 5w26). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w26:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5w26

Go back to Fluorine Binding Sites List in 5w26
Fluorine binding site 1 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:58.4
occ:1.00
 FAI A:9SG501 0.0 58.4 1.0
CAS A:9SG501 1.4 62.5 1.0
CAV A:9SG501 2.4 62.2 1.0
CAR A:9SG501 2.4 51.5 1.0
FAJ A:9SG501 2.7 69.7 1.0
OAM A:9SG501 2.9 53.2 1.0
CAT A:9SG501 3.0 52.9 1.0
O A:HOH895 3.3 43.0 1.0
CAU A:9SG501 3.5 56.2 1.0
CAO A:9SG501 3.8 56.9 1.0
OAE A:9SG501 4.2 52.4 1.0
NAL A:9SG501 4.4 49.1 1.0
OAG A:9SG501 4.5 50.3 1.0
CAQ A:9SG501 4.7 56.1 1.0
OAC A:9SG501 4.8 42.4 1.0
OD1 A:ASN399 4.9 42.4 1.0
OAB A:9SG501 4.9 52.1 1.0

Fluorine binding site 2 out of 4 in 5w26

Go back to Fluorine Binding Sites List in 5w26
Fluorine binding site 2 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:69.7
occ:1.00
 FAJ A:9SG501 0.0 69.7 1.0
CAV A:9SG501 1.3 62.2 1.0
OAM A:9SG501 2.2 53.2 1.0
CAO A:9SG501 2.3 56.9 1.0
CAS A:9SG501 2.4 62.5 1.0
FAI A:9SG501 2.7 58.4 1.0
OAE A:9SG501 3.0 52.4 1.0
OAC A:9SG501 3.1 42.4 1.0
O A:HOH895 3.2 43.0 1.0
CAU A:9SG501 3.6 56.2 1.0
CAR A:9SG501 3.8 51.5 1.0
OAF A:9SG501 4.1 55.5 1.0
CAT A:9SG501 4.2 52.9 1.0
CAP A:9SG501 4.5 58.2 1.0
CAQ A:9SG501 4.5 56.1 1.0
OAG A:9SG501 4.8 50.3 1.0

Fluorine binding site 3 out of 4 in 5w26

Go back to Fluorine Binding Sites List in 5w26
Fluorine binding site 3 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F514

b:45.4
occ:0.80
 F1 A:9WM514 0.0 45.4 0.8
F1 A:9VP515 1.2 15.7 0.2
C3 A:9WM514 1.4 29.5 0.8
C3 A:9VP515 2.2 14.4 0.2
C4 A:9WM514 2.3 25.7 0.8
C2 A:9WM514 2.3 24.8 0.8
C4 A:9VP515 2.5 14.0 0.2
OD1 A:ASP151 2.5 24.4 1.0
CG A:ASP151 2.8 30.4 1.0
C5 A:9VP515 2.9 13.9 0.2
OD2 A:ASP151 3.0 33.0 1.0
C5 A:9WM514 3.0 25.8 0.8
C1 A:9WM514 3.1 23.2 0.8
C2 A:9VP515 3.1 14.8 0.2
O6 A:9WM514 3.2 24.1 0.8
O6 A:9VP515 3.2 14.1 0.2
O1B A:9WM514 3.2 19.9 0.8
O A:HOH607 3.3 29.3 1.0
C1 A:9VP515 3.4 14.5 0.2
NH1 A:ARG118 3.4 19.5 1.0
O A:HOH960 3.5 48.5 1.0
O1B A:9VP515 3.5 14.4 0.2
OE2 A:GLU119 3.6 19.4 1.0
O A:HOH629 3.6 19.8 1.0
C6 A:9VP515 3.6 13.7 0.2
C6 A:9WM514 3.7 24.7 0.8
O A:HOH638 3.8 19.6 1.0
CB A:ASP151 3.9 26.7 1.0
O7 A:9VP515 4.1 13.2 0.2
O1A A:9VP515 4.2 14.3 0.2
O1A A:9WM514 4.2 21.6 0.8
N5 A:9VP515 4.2 13.9 0.2
N5 A:9WM514 4.3 27.1 0.8
OH A:TYR405 4.4 18.6 1.0
CZ A:ARG118 4.5 18.4 1.0
C7 A:9VP515 4.5 13.5 0.2
O A:HOH925 4.6 20.6 1.0
O7 A:9WM514 4.7 27.4 0.8
CD A:GLU119 4.8 21.6 1.0
O A:HOH894 4.9 46.2 1.0
C7 A:9WM514 4.9 26.6 0.8
NH2 A:ARG118 4.9 19.6 1.0
O A:HOH810 4.9 44.8 1.0
CA A:ASP151 4.9 26.8 1.0
O10 A:9WM514 5.0 29.0 0.8

Fluorine binding site 4 out of 4 in 5w26

Go back to Fluorine Binding Sites List in 5w26
Fluorine binding site 4 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Influenza Virus Neuraminidase N9 in Complex with 4-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F515

b:15.7
occ:0.20
 F1 A:9VP515 0.0 15.7 0.2
C3 A:9WM514 0.8 29.5 0.8
F1 A:9WM514 1.2 45.4 0.8
C3 A:9VP515 1.4 14.4 0.2
C2 A:9WM514 1.7 24.8 0.8
C2 A:9VP515 2.3 14.8 0.2
C4 A:9WM514 2.3 25.7 0.8
C1 A:9WM514 2.3 23.2 0.8
O1B A:9WM514 2.3 19.9 0.8
C4 A:9VP515 2.3 14.0 0.2
O1B A:9VP515 2.4 14.4 0.2
C1 A:9VP515 2.5 14.5 0.2
O6 A:9VP515 2.8 14.1 0.2
NH1 A:ARG118 2.9 19.5 1.0
O6 A:9WM514 3.0 24.1 0.8
C5 A:9VP515 3.1 13.9 0.2
C5 A:9WM514 3.3 25.8 0.8
OE2 A:GLU119 3.3 19.4 1.0
OD1 A:ASP151 3.5 24.4 1.0
OH A:TYR405 3.5 18.6 1.0
O1A A:9VP515 3.5 14.3 0.2
C6 A:9VP515 3.5 13.7 0.2
O1A A:9WM514 3.6 21.6 0.8
C6 A:9WM514 3.6 24.7 0.8
O A:HOH960 3.7 48.5 1.0
CZ A:ARG118 3.7 18.4 1.0
O A:HOH607 3.8 29.3 1.0
NH2 A:ARG118 3.9 19.6 1.0
CG A:ASP151 4.0 30.4 1.0
OD2 A:ASP151 4.1 33.0 1.0
CZ A:TYR405 4.1 18.0 1.0
O A:HOH638 4.2 19.6 1.0
O A:HOH629 4.3 19.8 1.0
N5 A:9VP515 4.5 13.9 0.2
O7 A:9VP515 4.5 13.2 0.2
CD A:GLU119 4.5 21.6 1.0
N5 A:9WM514 4.5 27.1 0.8
C7 A:9VP515 4.7 13.5 0.2
CE1 A:TYR405 4.7 19.3 1.0
CE2 A:TYR405 4.7 17.1 1.0
O A:HOH925 4.8 20.6 1.0
NE A:ARG118 4.9 16.9 1.0
O A:HOH894 4.9 46.2 1.0
CG A:GLU119 5.0 18.7 1.0
C7 A:9WM514 5.0 26.6 0.8
CB A:ASP151 5.0 26.7 1.0

Reference:

J.L.Mckimm-Breschkin, S.Barrett, P.A.Pilling, S.Hader, A.G.Watts, V.A.Streltsov. Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-Acetylneuraminic Acid Derivatives. J. Med. Chem. V. 61 1921 2018.
ISSN: ISSN 1520-4804
PubMed: 29397718
DOI: 10.1021/ACS.JMEDCHEM.7B01467
Page generated: Thu Aug 1 16:22:20 2024

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