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Fluorine in PDB 5w2y: Influenza Virus Neuraminidase N9 in Complex with 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

Enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid

All present enzymatic activity of Influenza Virus Neuraminidase N9 in Complex with 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid:
3.2.1.18;

Protein crystallography data

The structure of Influenza Virus Neuraminidase N9 in Complex with 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w2y 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) 48.48 / 2.39
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.383, 181.383, 181.383, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 19.8

Other elements in 5w2y:

The structure of Influenza Virus Neuraminidase N9 in Complex with 9-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 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid (pdb code 5w2y). 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 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid, PDB code: 5w2y:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5w2y

Go back to Fluorine Binding Sites List in 5w2y
Fluorine binding site 1 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 9-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 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:0.2
occ:1.00
 FAJ A:9T7501 0.0 0.2 1.0
CAV A:9T7501 1.3 94.0 1.0
OAM A:9T7501 2.2 1.0 1.0
CAO A:9T7501 2.3 74.4 1.0
CAS A:9T7501 2.4 98.1 1.0
FAI A:9T7501 2.5 87.5 1.0
OAE A:9T7501 2.9 54.1 1.0
OAC A:9T7501 3.0 55.0 1.0
CAU A:9T7501 3.6 98.5 1.0
CAR A:9T7501 3.7 92.8 1.0
CAT A:9T7501 4.0 95.1 1.0
OAF A:9T7501 4.2 95.6 1.0
CAP A:9T7501 4.5 91.8 1.0
CAQ A:9T7501 4.6 93.7 1.0
OAD A:9T7501 4.7 86.3 1.0

Fluorine binding site 2 out of 4 in 5w2y

Go back to Fluorine Binding Sites List in 5w2y
Fluorine binding site 2 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 9-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 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:87.5
occ:1.00
 FAI A:9T7501 0.0 87.5 1.0
CAS A:9T7501 1.4 98.1 1.0
CAR A:9T7501 2.4 92.8 1.0
CAV A:9T7501 2.4 94.0 1.0
FAJ A:9T7501 2.5 0.2 1.0
OAD A:9T7501 2.6 86.3 1.0
CAT A:9T7501 3.2 95.1 1.0
OAM A:9T7501 3.2 1.0 1.0
CAO A:9T7501 3.7 74.4 1.0
CAU A:9T7501 3.8 98.5 1.0
OAE A:9T7501 4.0 54.1 1.0
NAL A:9T7501 4.5 81.9 1.0
OD1 A:ASN399 4.5 41.4 1.0
OAC A:9T7501 4.7 55.0 1.0
CAQ A:9T7501 5.0 93.7 1.0

Fluorine binding site 3 out of 4 in 5w2y

Go back to Fluorine Binding Sites List in 5w2y
Fluorine binding site 3 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 9-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 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F515

b:37.2
occ:0.75
 F1 A:9TM515 0.0 37.2 0.8
C3 A:9TM515 1.4 28.7 0.8
F1 A:9T1516 2.1 17.8 0.2
C4 A:9T1516 2.1 16.8 0.2
C4 A:9TM515 2.3 27.5 0.8
C2 A:9TM515 2.3 27.6 0.8
O4 A:9T1516 2.4 16.6 0.2
C3 A:9T1516 2.4 17.1 0.2
OD1 A:ASP151 2.4 28.7 1.0
O4 A:9TM515 2.7 26.4 0.8
CG A:ASP151 2.8 31.7 1.0
C5 A:9T1516 2.8 16.5 0.2
C5 A:9TM515 2.8 26.6 0.8
O A:HOH887 2.9 36.8 1.0
O6 A:9TM515 3.2 29.0 0.8
C1 A:9TM515 3.2 25.6 0.8
OD2 A:ASP151 3.2 38.0 1.0
C2 A:9T1516 3.2 17.2 0.2
O1B A:9T1516 3.3 16.6 0.2
C1 A:9T1516 3.3 17.0 0.2
O6 A:9T1516 3.3 16.9 0.2
O1A A:9TM515 3.4 22.0 0.8
C6 A:9TM515 3.5 28.1 0.8
O A:HOH838 3.6 44.4 1.0
C6 A:9T1516 3.6 16.6 0.2
CB A:ASP151 3.7 27.3 1.0
OE2 A:GLU119 3.8 19.8 1.0
O A:HOH642 3.9 14.3 1.0
O A:HOH658 3.9 22.9 1.0
NH1 A:ARG118 3.9 19.8 1.0
N5 A:9T1516 4.1 16.0 0.2
N5 A:9TM515 4.1 23.6 0.8
O1A A:9T1516 4.2 16.8 0.2
O1B A:9TM515 4.2 23.9 0.8
O7 A:9T1516 4.3 16.4 0.2
OH A:TYR405 4.5 18.3 1.0
O10 A:9TM515 4.6 21.0 0.8
O7 A:9TM515 4.6 29.9 0.8
O10 A:9T1516 4.6 15.5 0.2
C7 A:9T1516 4.6 16.7 0.2
C7 A:9TM515 4.7 30.6 0.8
O A:HOH699 4.7 31.7 1.0
C10 A:9TM515 4.7 22.6 0.8
C10 A:9T1516 4.8 15.8 0.2
O A:HOH791 4.8 16.0 1.0
CA A:ASP151 4.8 25.2 1.0
CZ A:ARG118 4.8 19.8 1.0
CD A:GLU119 4.9 21.3 1.0

Fluorine binding site 4 out of 4 in 5w2y

Go back to Fluorine Binding Sites List in 5w2y
Fluorine binding site 4 out of 4 in the Influenza Virus Neuraminidase N9 in Complex with 9-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 9-Deoxygenated 2,3- Difluoro-N-Acetylneuraminic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F516

b:17.8
occ:0.25
 F1 A:9T1516 0.0 17.8 0.2
C3 A:9TM515 1.2 28.7 0.8
C3 A:9T1516 1.4 17.1 0.2
F1 A:9TM515 2.1 37.2 0.8
O1B A:9T1516 2.1 16.6 0.2
C4 A:9TM515 2.3 27.5 0.8
C2 A:9TM515 2.3 27.6 0.8
C4 A:9T1516 2.3 16.8 0.2
C2 A:9T1516 2.3 17.2 0.2
C1 A:9T1516 2.5 17.0 0.2
O1A A:9TM515 2.6 22.0 0.8
OE2 A:GLU119 2.7 19.8 1.0
O4 A:9T1516 2.7 16.6 0.2
C1 A:9TM515 2.8 25.6 0.8
O4 A:9TM515 2.8 26.4 0.8
NH1 A:ARG118 2.9 19.8 1.0
OH A:TYR405 3.2 18.3 1.0
NH2 A:ARG118 3.3 20.2 1.0
O6 A:9T1516 3.4 16.9 0.2
CZ A:ARG118 3.4 19.8 1.0
C5 A:9TM515 3.5 26.6 0.8
O6 A:9TM515 3.5 29.0 0.8
C5 A:9T1516 3.6 16.5 0.2
CZ A:TYR405 3.6 17.4 1.0
CD A:GLU119 3.7 21.3 1.0
O1A A:9T1516 3.7 16.8 0.2
OD1 A:ASP151 3.9 28.7 1.0
O1B A:9TM515 4.0 23.9 0.8
C6 A:9TM515 4.0 28.1 0.8
O A:HOH642 4.0 14.3 1.0
C6 A:9T1516 4.0 16.6 0.2
CG A:GLU119 4.0 20.6 1.0
CE2 A:TYR405 4.1 16.9 1.0
O A:HOH887 4.2 36.8 1.0
CE1 A:TYR405 4.2 17.9 1.0
NE A:ARG118 4.5 18.6 1.0
CG A:ASP151 4.6 31.7 1.0
N5 A:9TM515 4.6 23.6 0.8
N5 A:9T1516 4.7 16.0 0.2
OE1 A:GLU119 4.8 19.8 1.0
O A:HOH791 5.0 16.0 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: Tue Jul 15 08:47:39 2025

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