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Fluorine in PDB 5eir: Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.

Protein crystallography data

The structure of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor., PDB code: 5eir was solved by M.W.Nowicki, M.D.Walkinshaw, P.M.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.03 / 2.69
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 38.250, 52.120, 123.670, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 27.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. (pdb code 5eir). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor., PDB code: 5eir:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5eir

Go back to Fluorine Binding Sites List in 5eir
Fluorine binding site 1 out of 6 in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:43.1
occ:0.52
 FAH A:5O8301 0.0 43.1 0.5
O2 A:SO4302 1.0 44.2 0.5
CBG A:5O8301 1.3 48.1 0.5
S A:SO4302 1.4 51.0 0.5
O4 A:SO4302 2.0 46.9 0.5
O3 A:SO4302 2.0 41.8 0.5
FAG A:5O8301 2.2 47.5 0.5
FAI A:5O8301 2.2 41.0 0.5
O A:HOH413 2.4 26.2 1.0
SBH A:5O8301 2.6 54.1 0.5
O1 A:SO4302 2.7 46.8 0.5
NAS A:5O8301 3.1 40.2 0.5
OAC A:5O8301 3.2 43.2 0.5
C8 A:5O8301 3.5 36.4 0.5
O A:HOH416 3.6 30.5 1.0
C8 A:5O8301 3.6 36.4 0.5
NH2 A:ARG157 3.6 21.2 1.0
OAU A:5O8301 3.8 40.3 0.5
OAD A:5O8301 3.8 48.7 0.5
CAN A:5O8301 4.0 33.8 0.5
OD2 A:ASP90 4.1 14.4 1.0
ND2 A:ASN155 4.2 20.0 1.0
NE1 A:TRP56 4.3 23.1 1.0
CAM A:5O8301 4.4 33.6 0.5
N7 A:5O8301 4.4 35.5 0.5
CAQ A:5O8301 4.4 34.2 0.5
N9 A:5O8301 4.4 36.5 0.5
CAP A:5O8301 4.4 36.2 0.5
N7 A:5O8301 4.4 35.7 0.5
CAQ A:5O8301 4.5 34.2 0.5
CBD A:5O8301 4.5 39.1 0.5
N9 A:5O8301 4.6 36.4 0.5
CAW A:5O8301 4.7 34.6 0.5
CBC A:5O8301 4.8 34.7 0.5
CZ A:ARG157 4.8 17.5 1.0
CBD A:5O8301 4.9 38.9 0.5
CG A:ASN155 4.9 18.2 1.0
CAW A:5O8301 5.0 34.4 0.5
CAL A:5O8301 5.0 35.0 0.5
OAU A:5O8301 5.0 42.3 0.5

Fluorine binding site 2 out of 6 in 5eir

Go back to Fluorine Binding Sites List in 5eir
Fluorine binding site 2 out of 6 in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:51.5
occ:0.48
 FAH A:5O8301 0.0 51.5 0.5
CBG A:5O8301 1.3 43.1 0.5
FAI A:5O8301 2.2 38.5 0.5
FAG A:5O8301 2.2 42.2 0.5
SBH A:5O8301 2.6 34.8 0.5
CH2 A:TRP102 2.8 34.4 0.5
CB A:ALA204 2.9 37.2 1.0
CA A:ALA204 2.9 39.6 1.0
OAC A:5O8301 2.9 35.3 0.5
CAP A:5O8301 3.3 41.7 0.5
NAS A:5O8301 3.3 41.5 0.5
CZ3 A:TRP102 3.5 34.4 0.5
O A:THR203 3.5 51.9 1.0
CZ2 A:TRP102 3.5 36.2 0.5
N A:ALA204 3.6 37.8 1.0
OAD A:5O8301 3.8 35.7 0.5
C A:THR203 3.8 41.3 1.0
C A:ALA204 4.1 42.8 1.0
O A:ALA204 4.5 50.0 1.0
CE2 A:TRP102 4.6 32.6 0.5
CE3 A:TRP102 4.6 35.5 0.5
CBC A:5O8301 4.7 40.2 0.5
CG2 A:THR203 5.0 40.4 1.0
N A:THR205 5.0 41.4 1.0

Fluorine binding site 3 out of 6 in 5eir

Go back to Fluorine Binding Sites List in 5eir
Fluorine binding site 3 out of 6 in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:41.0
occ:0.52
 FAI A:5O8301 0.0 41.0 0.5
O3 A:SO4302 0.4 41.8 0.5
CBG A:5O8301 1.3 48.1 0.5
S A:SO4302 1.5 51.0 0.5
FAG A:5O8301 2.2 47.5 0.5
FAH A:5O8301 2.2 43.1 0.5
O1 A:SO4302 2.3 46.8 0.5
O2 A:SO4302 2.5 44.2 0.5
O4 A:SO4302 2.6 46.9 0.5
SBH A:5O8301 2.6 54.1 0.5
OAD A:5O8301 3.0 48.7 0.5
NH2 A:ARG157 3.1 21.2 1.0
NAS A:5O8301 3.3 40.2 0.5
NE A:ARG157 3.7 26.2 1.0
CZ A:ARG157 3.8 17.5 1.0
OAC A:5O8301 3.8 43.2 0.5
ND2 A:ASN155 4.1 20.0 1.0
O A:HOH413 4.2 26.2 1.0
CG A:ASN155 4.2 18.2 1.0
OD1 A:ASN155 4.5 20.6 1.0
NZ A:LYS162 4.6 43.1 1.0
CAP A:5O8301 4.6 36.2 0.5
CB A:ASN155 4.8 23.9 1.0
O A:HOH416 4.9 30.5 1.0
CD A:ARG157 5.0 26.4 1.0

Fluorine binding site 4 out of 6 in 5eir

Go back to Fluorine Binding Sites List in 5eir
Fluorine binding site 4 out of 6 in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:38.5
occ:0.48
 FAI A:5O8301 0.0 38.5 0.5
CBG A:5O8301 1.3 43.1 0.5
CB A:ALA204 2.1 37.2 1.0
FAH A:5O8301 2.2 51.5 0.5
FAG A:5O8301 2.2 42.2 0.5
CZ2 A:TRP102 2.4 36.2 0.5
SBH A:5O8301 2.6 34.8 0.5
CH2 A:TRP102 2.6 34.4 0.5
NAS A:5O8301 3.0 41.5 0.5
CA A:ALA204 3.1 39.6 1.0
CE2 A:TRP102 3.2 32.6 0.5
OAD A:5O8301 3.3 35.7 0.5
CZ2 A:TRP102 3.3 36.7 0.5
NE1 A:TRP102 3.5 29.6 0.5
CZ3 A:TRP102 3.6 34.4 0.5
CE2 A:TRP102 3.6 30.4 0.5
CAP A:5O8301 3.6 41.7 0.5
OAC A:5O8301 3.8 35.3 0.5
O A:ALA204 4.0 50.0 1.0
NE1 A:TRP102 4.0 32.9 0.5
C A:ALA204 4.0 42.8 1.0
CD2 A:TRP102 4.0 30.6 0.5
N A:ALA204 4.1 37.8 1.0
CE3 A:TRP102 4.2 35.5 0.5
CH2 A:TRP102 4.3 31.7 0.5
CD1 A:TRP102 4.6 28.5 0.5
CD2 A:TRP102 4.8 27.1 0.5
C A:THR203 5.0 41.3 1.0

Fluorine binding site 5 out of 6 in 5eir

Go back to Fluorine Binding Sites List in 5eir
Fluorine binding site 5 out of 6 in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:47.5
occ:0.52
 FAG A:5O8301 0.0 47.5 0.5
O1 A:SO4302 0.6 46.8 0.5
S A:SO4302 1.0 51.0 0.5
CBG A:5O8301 1.3 48.1 0.5
O2 A:SO4302 1.8 44.2 0.5
O4 A:SO4302 2.0 46.9 0.5
FAI A:5O8301 2.2 41.0 0.5
FAH A:5O8301 2.2 43.1 0.5
O3 A:SO4302 2.2 41.8 0.5
SBH A:5O8301 2.6 54.1 0.5
OAC A:5O8301 3.0 43.2 0.5
CAN A:5O8301 3.1 33.8 0.5
OAD A:5O8301 3.2 48.7 0.5
CAM A:5O8301 3.4 33.6 0.5
CAL A:5O8301 3.5 35.0 0.5
NAS A:5O8301 4.0 40.2 0.5
CAK A:5O8301 4.0 35.0 0.5
O A:HOH416 4.1 30.5 1.0
C8 A:5O8301 4.2 36.4 0.5
CAW A:5O8301 4.3 34.6 0.5
C8 A:5O8301 4.3 36.4 0.5
OD1 A:ASN155 4.5 20.6 1.0
CAW A:5O8301 4.5 34.4 0.5
ND2 A:ASN155 4.5 20.0 1.0
O A:HOH413 4.6 26.2 1.0
CG A:ASN155 4.7 18.2 1.0
CAQ A:5O8301 4.7 34.2 0.5
CAQ A:5O8301 4.8 34.2 0.5
CAJ A:5O8301 4.9 33.2 0.5
N7 A:5O8301 4.9 35.5 0.5
OAU A:5O8301 4.9 40.3 0.5
NZ A:LYS162 4.9 43.1 1.0
NH2 A:ARG157 4.9 21.2 1.0
NH2 A:ARG112 4.9 31.8 1.0
N7 A:5O8301 4.9 35.7 0.5

Fluorine binding site 6 out of 6 in 5eir

Go back to Fluorine Binding Sites List in 5eir
Fluorine binding site 6 out of 6 in the Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Co-Crystal Structure of EIF4E with Nucleotide Mimetic Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:42.2
occ:0.48
 FAG A:5O8301 0.0 42.2 0.5
CBG A:5O8301 1.3 43.1 0.5
CB A:ALA204 2.1 37.2 1.0
CZ3 A:TRP102 2.1 34.4 0.5
CH2 A:TRP102 2.1 34.4 0.5
FAI A:5O8301 2.2 38.5 0.5
FAH A:5O8301 2.2 51.5 0.5
SBH A:5O8301 2.6 34.8 0.5
CZ2 A:TRP102 2.8 36.2 0.5
CE3 A:TRP102 2.8 35.5 0.5
CA A:ALA204 2.8 39.6 1.0
OAD A:5O8301 2.9 35.7 0.5
N A:ALA204 3.0 37.8 1.0
OAC A:5O8301 3.3 35.3 0.5
CE2 A:TRP102 3.3 32.6 0.5
CD2 A:TRP102 3.3 30.6 0.5
NE1 A:TRP102 3.5 29.6 0.5
C A:THR203 3.7 41.3 1.0
CE2 A:TRP102 3.8 30.4 0.5
O A:HIS200 3.9 30.0 1.0
NAS A:5O8301 3.9 41.5 0.5
CZ2 A:TRP102 4.0 36.7 0.5
O A:THR203 4.1 51.9 1.0
CD1 A:TRP102 4.1 28.5 0.5
CB A:THR203 4.3 23.6 1.0
C A:ALA204 4.3 42.8 1.0
CAK A:5O8301 4.4 32.0 0.5
NE1 A:TRP102 4.5 32.9 0.5
CD2 A:TRP102 4.5 27.1 0.5
CG2 A:THR203 4.5 40.4 1.0
CG A:TRP102 4.5 28.9 0.5
CA A:THR203 4.6 34.8 1.0
CAP A:5O8301 4.6 41.7 0.5
CG A:TRP102 4.7 29.3 0.5
CAL A:5O8301 4.7 32.1 0.5
CAJ A:5O8301 4.7 33.2 0.5
O A:ALA204 4.8 50.0 1.0
CAJ A:5O8301 4.9 32.5 0.5
CAM A:5O8301 4.9 34.7 0.5
CH2 A:TRP102 4.9 31.7 0.5

Reference:

F.Soukarieh, M.W.Nowicki, A.Bastide, T.Poyry, C.Jones, K.Dudek, G.Patwardhan, F.Meullenet, N.J.Oldham, M.D.Walkinshaw, A.E.Willis, P.M.Fischer. Design of Nucleotide-Mimetic and Non-Nucleotide Inhibitors of the Translation Initiation Factor EIF4E: Synthesis, Structural and Functional Characterisation. Eur.J.Med.Chem. V. 124 200 2016.
ISSN: ISSN 0223-5234
PubMed: 27592390
DOI: 10.1016/J.EJMECH.2016.08.047
Page generated: Thu Aug 1 09:03:26 2024

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