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Fluorine in PDB 3sjo: Structure of EV71 3C in Complex with Rupintrivir (AG7088)

Enzymatic activity of Structure of EV71 3C in Complex with Rupintrivir (AG7088)

All present enzymatic activity of Structure of EV71 3C in Complex with Rupintrivir (AG7088):
3.4.22.28;

Protein crystallography data

The structure of Structure of EV71 3C in Complex with Rupintrivir (AG7088), PDB code: 3sjo was solved by G.Lu, J.Qi, Z.Chen, X.Xu, F.Gao, D.Lin, W.Qian, H.Liu, H.Jiang, J.Yan, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.54 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.258, 82.171, 97.952, 89.96, 89.99, 90.13
R / Rfree (%) 20.5 / 22.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of EV71 3C in Complex with Rupintrivir (AG7088) (pdb code 3sjo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of EV71 3C in Complex with Rupintrivir (AG7088), PDB code: 3sjo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3sjo

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Fluorine binding site 1 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.9
occ:1.00
 F1 A:AG7501 0.0 28.9 1.0
C09 A:AG7501 1.3 23.9 1.0
C08 A:AG7501 2.4 21.5 1.0
C10 A:AG7501 2.5 26.4 1.0
CD A:LYS130 3.1 30.5 1.0
NH2 A:ARG39 3.1 39.4 1.0
CB A:LYS130 3.5 26.6 1.0
C07 A:AG7501 3.7 22.7 1.0
O A:LEU127 3.8 17.9 1.0
C11 A:AG7501 3.8 24.2 1.0
CG A:LYS130 3.9 26.5 1.0
CE A:LYS130 4.1 37.4 1.0
CZ A:ARG39 4.2 27.3 1.0
C06 A:AG7501 4.2 22.1 1.0
O A:HOH580 4.3 26.4 1.0
NZ A:LYS130 4.6 36.3 1.0
OE1 A:GLU71 4.6 19.5 1.0
NH1 A:ARG39 4.8 21.6 1.0
CA A:LYS130 4.8 27.1 1.0
CB A:SER128 4.9 33.4 1.0
C A:LEU127 4.9 23.0 1.0
CG A:LEU127 4.9 16.8 1.0

Fluorine binding site 2 out of 8 in 3sjo

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Fluorine binding site 2 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:38.4
occ:1.00
 F1 B:AG7501 0.0 38.4 1.0
C09 B:AG7501 1.3 34.1 1.0
C08 B:AG7501 2.4 35.9 1.0
C10 B:AG7501 2.4 36.7 1.0
CD B:LYS130 3.0 24.3 1.0
CB B:LYS130 3.1 22.9 1.0
NH2 B:ARG39 3.6 45.6 1.0
CG B:LYS130 3.6 23.5 1.0
NH1 B:ARG39 3.6 39.7 1.0
O B:LEU127 3.7 25.4 1.0
C07 B:AG7501 3.7 30.7 1.0
C11 B:AG7501 3.8 36.2 1.0
CZ B:ARG39 3.9 40.6 1.0
C06 B:AG7501 4.2 34.1 1.0
CE B:LYS130 4.3 28.6 1.0
CA B:LYS130 4.5 18.8 1.0
OE1 B:GLU71 4.6 20.9 1.0
N B:LYS130 4.8 22.3 1.0
C B:LEU127 4.8 25.8 1.0

Fluorine binding site 3 out of 8 in 3sjo

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Fluorine binding site 3 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:28.5
occ:1.00
 F1 C:AG7501 0.0 28.5 1.0
C09 C:AG7501 1.3 27.8 1.0
C08 C:AG7501 2.4 22.3 1.0
O C:HOH230 2.4 25.5 1.0
C10 C:AG7501 2.4 29.1 1.0
NH1 C:ARG39 3.1 24.5 1.0
CB C:LYS130 3.3 25.2 1.0
CD C:LYS130 3.4 31.6 1.0
O C:LEU127 3.7 27.8 1.0
C07 C:AG7501 3.7 24.9 1.0
C11 C:AG7501 3.8 27.2 1.0
CG C:LYS130 4.0 27.3 1.0
C06 C:AG7501 4.2 23.3 1.0
CZ C:ARG39 4.4 23.6 1.0
O C:HOH226 4.4 25.5 1.0
OE1 C:GLU71 4.5 18.8 1.0
CE C:LYS130 4.6 37.9 1.0
CA C:LYS130 4.7 29.2 1.0
CB C:SER128 4.7 32.0 1.0
C C:LEU127 4.8 25.1 1.0
N C:LYS130 4.8 29.2 1.0
CG C:LEU127 5.0 18.4 1.0

Fluorine binding site 4 out of 8 in 3sjo

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Fluorine binding site 4 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:24.5
occ:1.00
 F1 D:AG7501 0.0 24.5 1.0
C09 D:AG7501 1.3 20.3 1.0
C08 D:AG7501 2.3 18.6 1.0
C10 D:AG7501 2.5 21.6 1.0
NH2 D:ARG39 2.9 22.4 1.0
CD D:LYS130 3.2 22.8 1.0
CB D:LYS130 3.4 22.5 1.0
O D:HOH216 3.6 25.5 1.0
O D:LEU127 3.7 18.5 1.0
C07 D:AG7501 3.7 20.2 1.0
C11 D:AG7501 3.8 20.2 1.0
CG D:LYS130 3.9 19.2 1.0
CZ D:ARG39 4.1 24.1 1.0
C06 D:AG7501 4.2 18.5 1.0
CE D:LYS130 4.4 29.7 1.0
O D:HOH296 4.6 25.5 1.0
OE1 D:GLU71 4.6 17.8 1.0
C D:LEU127 4.8 22.6 1.0
CB D:SER128 4.8 20.4 1.0
CA D:LYS130 4.8 21.2 1.0
NH1 D:ARG39 4.8 24.8 1.0
CG D:LEU127 4.9 15.8 1.0
NZ D:LYS130 4.9 30.5 1.0
NE D:ARG39 4.9 20.5 1.0
O D:SER128 5.0 24.3 1.0

Fluorine binding site 5 out of 8 in 3sjo

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Fluorine binding site 5 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:33.0
occ:1.00
 F1 E:AG7501 0.0 33.0 1.0
C09 E:AG7501 1.3 30.8 1.0
C08 E:AG7501 2.4 24.6 1.0
C10 E:AG7501 2.4 31.5 1.0
CB E:LYS130 3.3 23.6 1.0
CD E:LYS130 3.3 29.2 1.0
NH1 E:ARG39 3.7 26.6 1.0
C07 E:AG7501 3.7 24.9 1.0
O E:LEU127 3.7 26.7 1.0
C11 E:AG7501 3.8 30.3 1.0
CG E:LYS130 3.9 25.2 1.0
O E:HOH214 4.1 25.5 1.0
C06 E:AG7501 4.2 25.4 1.0
OE1 E:GLU71 4.4 20.4 1.0
NH2 E:ARG39 4.4 31.8 1.0
CZ E:ARG39 4.4 30.1 1.0
CA E:LYS130 4.7 26.6 1.0
CE E:LYS130 4.7 34.2 1.0
CB E:SER128 4.8 26.2 1.0
C E:LEU127 4.8 22.6 1.0
N E:LYS130 4.8 28.4 1.0
CG E:LEU127 4.9 17.6 1.0
CD2 E:HIS40 4.9 25.4 1.0

Fluorine binding site 6 out of 8 in 3sjo

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Fluorine binding site 6 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F501

b:37.1
occ:1.00
 F1 F:AG7501 0.0 37.1 1.0
C09 F:AG7501 1.3 32.1 1.0
C08 F:AG7501 2.4 34.4 1.0
C10 F:AG7501 2.5 37.8 1.0
CB F:LYS130 3.2 31.7 1.0
CD F:LYS130 3.3 37.2 1.0
NH1 F:ARG39 3.5 32.1 1.0
O F:HOH601 3.6 26.4 1.0
NH2 F:ARG39 3.7 44.0 1.0
O F:LEU127 3.7 25.7 1.0
C07 F:AG7501 3.7 29.1 1.0
CG F:LYS130 3.7 32.7 1.0
C11 F:AG7501 3.8 35.5 1.0
CE F:LYS130 3.9 39.1 1.0
CZ F:ARG39 3.9 37.0 1.0
C06 F:AG7501 4.3 33.2 1.0
CA F:LYS130 4.5 31.8 1.0
NZ F:LYS130 4.6 42.6 1.0
OE1 F:GLU71 4.6 27.6 1.0
N F:LYS130 4.7 30.1 1.0
C F:LEU127 4.8 27.6 1.0
CG F:LEU127 5.0 25.7 1.0

Fluorine binding site 7 out of 8 in 3sjo

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Fluorine binding site 7 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F501

b:33.5
occ:1.00
 F1 G:AG7501 0.0 33.5 1.0
C09 G:AG7501 1.3 35.4 1.0
C08 G:AG7501 2.4 34.8 1.0
C10 G:AG7501 2.4 35.9 1.0
CD G:LYS130 3.1 33.0 1.0
NH2 G:ARG39 3.1 39.3 1.0
CB G:LYS130 3.2 27.6 1.0
C07 G:AG7501 3.7 30.2 1.0
CG G:LYS130 3.7 32.9 1.0
C11 G:AG7501 3.8 29.9 1.0
O G:LEU127 3.8 25.2 1.0
CE G:LYS130 4.2 38.6 1.0
C06 G:AG7501 4.2 27.6 1.0
CZ G:ARG39 4.3 37.7 1.0
CA G:LYS130 4.6 30.6 1.0
NZ G:LYS130 4.6 43.6 1.0
NH1 G:ARG39 4.7 38.1 1.0
N G:LYS130 4.8 28.0 1.0
CB G:SER128 4.9 0.3 1.0
O G:SER128 4.9 0.2 1.0
C G:LEU127 4.9 27.0 1.0
OE1 G:GLU71 5.0 31.8 1.0

Fluorine binding site 8 out of 8 in 3sjo

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Fluorine binding site 8 out of 8 in the Structure of EV71 3C in Complex with Rupintrivir (AG7088)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of EV71 3C in Complex with Rupintrivir (AG7088) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F501

b:33.4
occ:1.00
 F1 H:AG7501 0.0 33.4 1.0
C09 H:AG7501 1.3 35.3 1.0
C08 H:AG7501 2.4 32.4 1.0
C10 H:AG7501 2.4 37.7 1.0
NH2 H:ARG39 3.1 35.4 1.0
CD H:LYS130 3.1 38.2 1.0
CB H:LYS130 3.2 33.1 1.0
C07 H:AG7501 3.7 28.1 1.0
O H:LEU127 3.7 26.7 1.0
CG H:LYS130 3.7 35.7 1.0
O H:HOH263 3.7 25.5 1.0
C11 H:AG7501 3.8 28.8 1.0
C06 H:AG7501 4.2 28.7 1.0
CZ H:ARG39 4.3 32.9 1.0
CE H:LYS130 4.4 44.0 1.0
CA H:LYS130 4.5 33.8 1.0
N H:LYS130 4.7 30.8 1.0
OE1 H:GLU71 4.8 28.0 1.0
NH1 H:ARG39 4.8 30.2 1.0
C H:LEU127 4.8 29.2 1.0
O H:SER128 4.9 25.4 1.0
CB H:SER128 4.9 22.7 1.0
NZ H:LYS130 4.9 45.2 1.0

Reference:

G.Lu, J.Qi, Z.Chen, X.Xu, F.Gao, D.Lin, W.Qian, H.Liu, H.Jiang, J.Yan, G.F.Gao. Enterovirus 71 and Coxsackievirus A16 3C Proteases: Binding to Rupintrivir and Their Substrates and Anti-Hand, Foot, and Mouth Disease Virus Drug Design. J.Virol. V. 85 10319 2011.
ISSN: ISSN 0022-538X
PubMed: 21795339
DOI: 10.1128/JVI.00787-11
Page generated: Sun Dec 13 11:55:17 2020

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