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Fluorine in PDB 5w2u: Influenza Virus Neuraminidase N9 in Complex with 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

Enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

All present enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid:
3.2.1.18;

Protein crystallography data

The structure of Influenza Virus Neuraminidase N9 in Complex with 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w2u 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) 48.38 / 2.00
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.025, 181.025, 181.025, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.7

Other elements in 5w2u:

The structure of Influenza Virus Neuraminidase N9 in Complex with 7-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 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid (pdb code 5w2u). 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 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w2u:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5w2u

Go back to Fluorine Binding Sites List in 5w2u
Fluorine binding site 1 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 7-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 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:46.9
occ:1.00
 FAJ A:9SM501 0.0 46.9 1.0
CAV A:9SM501 1.3 41.8 1.0
OAM A:9SM501 2.1 39.1 1.0
CAS A:9SM501 2.3 42.0 1.0
CAO A:9SM501 2.3 43.1 1.0
FAI A:9SM501 2.5 38.1 1.0
OAC A:9SM501 3.0 39.5 1.0
OAE A:9SM501 3.1 41.0 1.0
O A:HOH947 3.2 56.6 1.0
CAU A:9SM501 3.4 41.7 1.0
CAR A:9SM501 3.6 34.7 1.0
OAF A:9SM501 3.9 42.8 1.0
CAT A:9SM501 4.0 35.8 1.0
CAP A:9SM501 4.2 42.1 1.0
CAQ A:9SM501 4.3 35.1 1.0
OAG A:9SM501 4.6 38.6 1.0

Fluorine binding site 2 out of 4 in 5w2u

Go back to Fluorine Binding Sites List in 5w2u
Fluorine binding site 2 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 7-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 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:38.1
occ:1.00
 FAI A:9SM501 0.0 38.1 1.0
CAS A:9SM501 1.4 42.0 1.0
CAV A:9SM501 2.3 41.8 1.0
CAR A:9SM501 2.5 34.7 1.0
FAJ A:9SM501 2.5 46.9 1.0
OAG A:9SM501 2.7 38.6 1.0
OAM A:9SM501 2.8 39.1 1.0
CAT A:9SM501 3.1 35.8 1.0
O A:HOH947 3.3 56.6 1.0
CAU A:9SM501 3.5 41.7 1.0
CAO A:9SM501 3.7 43.1 1.0
OAE A:9SM501 4.0 41.0 1.0
NAL A:9SM501 4.4 31.1 1.0
CAQ A:9SM501 4.6 35.1 1.0
OAC A:9SM501 4.7 39.5 1.0
OD1 A:ASN399 5.0 33.3 1.0

Fluorine binding site 3 out of 4 in 5w2u

Go back to Fluorine Binding Sites List in 5w2u
Fluorine binding site 3 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 7-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 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F514

b:45.8
occ:0.55
 F1 A:9S4514 0.0 45.8 0.6
F1 A:9SJ515 1.3 25.0 0.5
C3 A:9S4514 1.4 30.8 0.6
C2 A:9S4514 2.3 26.7 0.6
C4 A:9S4514 2.4 27.7 0.6
OD1 A:ASP151 2.4 27.8 1.0
C3 A:9SJ515 2.5 22.4 0.5
O4 A:9S4514 2.5 25.2 0.6
CG A:ASP151 2.8 28.6 1.0
O4 A:9SJ515 2.8 20.5 0.5
C4 A:9SJ515 3.0 20.9 0.5
OD2 A:ASP151 3.0 31.5 1.0
C1 A:9S4514 3.1 25.0 0.6
C5 A:9S4514 3.1 26.7 0.6
O1A A:9S4514 3.2 21.6 0.6
O1B A:9SJ515 3.2 21.6 0.5
O6 A:9S4514 3.3 25.6 0.6
C5 A:9SJ515 3.3 21.7 0.5
C1 A:9SJ515 3.3 22.2 0.5
C2 A:9SJ515 3.4 22.9 0.5
NH1 A:ARG118 3.5 20.3 1.0
O A:HOH625 3.5 25.6 1.0
O6 A:9SJ515 3.5 22.6 0.5
OE2 A:GLU119 3.6 20.5 1.0
O A:HOH606 3.6 22.6 1.0
O A:HOH973 3.7 50.1 1.0
C6 A:9S4514 3.8 26.2 0.6
CB A:ASP151 3.8 23.7 1.0
C6 A:9SJ515 4.1 21.4 0.5
O1A A:9SJ515 4.1 20.5 0.5
O1B A:9S4514 4.2 25.3 0.6
O A:HOH952 4.2 55.9 1.0
N5 A:9S4514 4.4 27.9 0.6
CZ A:ARG118 4.5 21.7 1.0
O A:HOH903 4.6 22.0 1.0
N5 A:9SJ515 4.6 21.6 0.5
OH A:TYR405 4.6 20.3 1.0
CD A:GLU119 4.7 22.1 1.0
CA A:ASP151 4.8 25.2 1.0
O10 A:9SJ515 4.9 20.8 0.5
O A:HOH667 4.9 22.7 1.0
NH2 A:ARG118 4.9 17.6 1.0
C7 A:9S4514 5.0 26.3 0.6
O10 A:9S4514 5.0 26.1 0.6
C7 A:9SJ515 5.0 21.8 0.5

Fluorine binding site 4 out of 4 in 5w2u

Go back to Fluorine Binding Sites List in 5w2u
Fluorine binding site 4 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 7-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 7-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F515

b:25.0
occ:0.45
 F1 A:9SJ515 0.0 25.0 0.5
C3 A:9S4514 0.3 30.8 0.6
C2 A:9S4514 1.3 26.7 0.6
F1 A:9S4514 1.3 45.8 0.6
C3 A:9SJ515 1.3 22.4 0.5
C4 A:9S4514 1.8 27.7 0.6
C2 A:9SJ515 2.1 22.9 0.5
C1 A:9S4514 2.2 25.0 0.6
C1 A:9SJ515 2.3 22.2 0.5
C4 A:9SJ515 2.3 20.9 0.5
O1B A:9SJ515 2.4 21.6 0.5
O6 A:9S4514 2.5 25.6 0.6
O6 A:9SJ515 2.5 22.6 0.5
O1A A:9S4514 2.6 21.6 0.6
O4 A:9S4514 2.6 25.2 0.6
O4 A:9SJ515 2.7 20.5 0.5
C5 A:9S4514 2.7 26.7 0.6
C5 A:9SJ515 2.8 21.7 0.5
C6 A:9S4514 3.0 26.2 0.6
O1A A:9SJ515 3.2 20.5 0.5
C6 A:9SJ515 3.2 21.4 0.5
OH A:TYR405 3.3 20.3 1.0
O1B A:9S4514 3.3 25.3 0.6
NH1 A:ARG118 3.6 20.3 1.0
OE2 A:GLU119 3.6 20.5 1.0
OD1 A:ASP151 3.7 27.8 1.0
CG A:ASP151 4.0 28.6 1.0
N5 A:9S4514 4.0 27.9 0.6
CZ A:TYR405 4.1 19.2 1.0
OD2 A:ASP151 4.1 31.5 1.0
N5 A:9SJ515 4.2 21.6 0.5
O A:HOH973 4.2 50.1 1.0
CZ A:ARG118 4.3 21.7 1.0
C7 A:9SJ515 4.4 21.8 0.5
NH2 A:ARG118 4.4 17.6 1.0
O A:HOH952 4.4 55.9 1.0
O A:HOH606 4.4 22.6 1.0
C7 A:9S4514 4.4 26.3 0.6
O A:HOH625 4.6 25.6 1.0
CD A:GLU119 4.6 22.1 1.0
CE2 A:TYR405 4.7 20.4 1.0
CE1 A:TYR405 4.8 19.7 1.0
CB A:ASP151 4.8 23.7 1.0
O A:HOH848 4.8 46.6 1.0
OE2 A:GLU278 4.9 35.0 1.0
CG A:GLU119 5.0 19.2 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 16:22:30 2024

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