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Fluorine in PDB 5qde: Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A:
3.1.3.48;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A, PDB code: 5qde was solved by D.A.Keedy, Z.B.Hill, J.T.Biel, E.Kang, T.J.Rettenmaier, J.Brandao-Neto, F.Von Delft, J.A.Wells, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.82 / 1.76
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.839, 89.839, 106.494, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A (pdb code 5qde). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A, PDB code: 5qde:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5qde

Go back to Fluorine Binding Sites List in 5qde
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.3
occ:0.12
F1 A:AWD401 0.0 30.3 0.1
F1 A:AWD401 0.0 30.3 0.1
C10 A:AWD401 1.3 20.4 0.1
C10 A:AWD401 1.3 20.4 0.1
C11 A:AWD401 2.4 35.7 0.1
C11 A:AWD401 2.4 35.7 0.1
C9 A:AWD401 2.4 20.1 0.1
C9 A:AWD401 2.4 20.1 0.1
HD3 A:ARG169 2.5 44.5 0.4
HD3 A:ARG169 2.5 44.5 0.4
HA A:LYS103 2.6 28.6 1.0
H15 A:AWD401 2.6 24.1 0.1
H15 A:AWD401 2.6 24.1 0.1
H16 A:AWD401 2.7 42.8 0.1
H16 A:AWD401 2.7 42.8 0.1
HD3 A:ARG169 2.7 44.4 0.1
HD3 A:ARG169 2.7 44.4 0.1
O A:LYS103 3.0 24.6 1.0
HH11 A:ARG169 3.0 38.4 0.4
HH11 A:ARG169 3.0 38.4 0.4
O A:HOH631 3.0 26.4 1.0
O A:HOH589 3.0 45.1 0.4
O A:HOH589 3.0 45.1 0.4
HB3 A:LYS103 3.1 33.0 1.0
C A:LYS103 3.1 22.6 1.0
HH11 A:ARG169 3.1 41.0 0.1
HH11 A:ARG169 3.1 41.0 0.1
CA A:LYS103 3.2 23.9 1.0
CD A:ARG169 3.3 37.1 0.4
CD A:ARG169 3.3 37.1 0.4
NH1 A:ARG169 3.4 32.0 0.4
NH1 A:ARG169 3.4 32.0 0.4
O A:HOH589 3.5 31.0 0.1
O A:HOH589 3.5 30.9 0.1
CD A:ARG169 3.5 37.0 0.1
CD A:ARG169 3.5 37.0 0.1
O A:SER104 3.5 24.9 1.0
HD2 A:ARG169 3.5 44.5 0.4
HD2 A:ARG169 3.5 44.5 0.4
NH1 A:ARG169 3.6 34.1 0.1
NH1 A:ARG169 3.6 34.1 0.1
HD2 A:ARG169 3.6 44.4 0.1
HD2 A:ARG169 3.6 44.4 0.1
CB A:LYS103 3.6 27.5 1.0
C12 A:AWD401 3.7 28.3 0.1
C12 A:AWD401 3.7 28.3 0.1
C8 A:AWD401 3.7 19.1 0.1
C8 A:AWD401 3.7 19.1 0.1
NE A:ARG169 3.8 37.4 0.4
NE A:ARG169 3.8 37.4 0.4
CZ A:ARG169 3.9 42.3 0.4
CZ A:ARG169 3.9 42.3 0.4
HH12 A:ARG169 3.9 38.4 0.4
HH12 A:ARG169 3.9 38.4 0.4
N A:SER104 3.9 20.6 1.0
NE A:ARG169 4.0 37.0 0.1
NE A:ARG169 4.0 37.0 0.1
HG2 A:LYS103 4.0 34.7 1.0
CZ A:ARG169 4.0 40.4 0.1
CZ A:ARG169 4.0 40.4 0.1
HH12 A:ARG169 4.0 41.0 0.1
HH12 A:ARG169 4.0 41.0 0.1
C A:SER104 4.1 19.5 1.0
C7 A:AWD401 4.2 37.4 0.1
C7 A:AWD401 4.2 37.4 0.1
H A:SER104 4.4 24.7 1.0
CG A:LYS103 4.4 28.9 1.0
HB2 A:LYS103 4.4 33.0 1.0
HG2 A:ARG169 4.4 48.7 0.4
HG2 A:ARG169 4.4 48.7 0.4
HA A:ARG105 4.4 27.8 0.1
HA A:ARG105 4.4 27.8 0.1
CG A:ARG169 4.5 40.6 0.4
CG A:ARG169 4.5 40.6 0.4
HA A:ARG105 4.5 28.1 0.4
H17 A:AWD401 4.5 34.0 0.1
H17 A:AWD401 4.5 34.0 0.1
HE A:ARG169 4.5 44.9 0.4
HE A:ARG169 4.5 44.9 0.4
HD1 A:HIS208 4.5 34.4 0.1
HD1 A:HIS208 4.5 34.4 0.1
N A:LYS103 4.6 22.4 1.0
H7 A:AWD401 4.6 22.9 0.1
H7 A:AWD401 4.6 22.9 0.1
CA A:SER104 4.6 19.7 1.0
HB3 A:ARG169 4.6 38.3 0.1
HB3 A:ARG169 4.6 38.3 0.1
HB3 A:ARG169 4.6 38.5 0.4
HB3 A:ARG169 4.6 38.5 0.4
HA A:ARG105 4.6 27.6 0.4
HE A:ARG169 4.7 44.4 0.1
HE A:ARG169 4.7 44.4 0.1
HD1 A:HIS208 4.7 34.8 0.4
HD1 A:HIS208 4.7 34.8 0.4
H A:GLY209 4.7 32.1 1.0
CG A:ARG169 4.8 34.4 0.1
CG A:ARG169 4.8 34.4 0.1
N A:ARG105 4.8 19.9 0.4
N A:ARG105 4.9 20.1 0.1
N A:ARG105 4.9 20.1 0.1
N A:ARG105 4.9 19.9 0.4
HG2 A:ARG169 4.9 41.2 0.1
HG2 A:ARG169 4.9 41.2 0.1
NH2 A:ARG169 4.9 37.5 0.4
NH2 A:ARG169 4.9 37.5 0.4
H A:LYS103 4.9 26.9 1.0
HD12 A:ILE171 5.0 33.2 0.4
HD12 A:ILE171 5.0 33.2 0.4

Fluorine binding site 2 out of 2 in 5qde

Go back to Fluorine Binding Sites List in 5qde
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000740A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.3
occ:0.12
F1 A:AWD401 0.0 30.3 0.1
F1 A:AWD401 0.0 30.3 0.1
C10 A:AWD401 1.3 20.4 0.1
C10 A:AWD401 1.3 20.4 0.1
C11 A:AWD401 2.4 35.7 0.1
C11 A:AWD401 2.4 35.7 0.1
C9 A:AWD401 2.4 20.1 0.1
C9 A:AWD401 2.4 20.1 0.1
HD3 A:ARG169 2.5 44.5 0.4
HD3 A:ARG169 2.5 44.5 0.4
HA A:LYS103 2.6 28.6 1.0
H15 A:AWD401 2.6 24.1 0.1
H15 A:AWD401 2.6 24.1 0.1
H16 A:AWD401 2.7 42.8 0.1
H16 A:AWD401 2.7 42.8 0.1
HD3 A:ARG169 2.7 44.4 0.1
HD3 A:ARG169 2.7 44.4 0.1
O A:LYS103 3.0 24.6 1.0
HH11 A:ARG169 3.0 38.4 0.4
HH11 A:ARG169 3.0 38.4 0.4
O A:HOH631 3.0 26.4 1.0
O A:HOH589 3.0 45.1 0.4
O A:HOH589 3.0 45.1 0.4
HB3 A:LYS103 3.1 33.0 1.0
C A:LYS103 3.1 22.6 1.0
HH11 A:ARG169 3.1 41.0 0.1
HH11 A:ARG169 3.1 41.0 0.1
CA A:LYS103 3.2 23.9 1.0
CD A:ARG169 3.3 37.1 0.4
CD A:ARG169 3.3 37.1 0.4
NH1 A:ARG169 3.4 32.0 0.4
NH1 A:ARG169 3.4 32.0 0.4
O A:HOH589 3.5 31.0 0.1
O A:HOH589 3.5 30.9 0.1
CD A:ARG169 3.5 37.0 0.1
CD A:ARG169 3.5 37.0 0.1
O A:SER104 3.5 24.9 1.0
HD2 A:ARG169 3.5 44.5 0.4
HD2 A:ARG169 3.5 44.5 0.4
NH1 A:ARG169 3.6 34.1 0.1
NH1 A:ARG169 3.6 34.1 0.1
HD2 A:ARG169 3.6 44.4 0.1
HD2 A:ARG169 3.6 44.4 0.1
CB A:LYS103 3.6 27.5 1.0
C12 A:AWD401 3.7 28.3 0.1
C12 A:AWD401 3.7 28.3 0.1
C8 A:AWD401 3.7 19.1 0.1
C8 A:AWD401 3.7 19.1 0.1
NE A:ARG169 3.8 37.4 0.4
NE A:ARG169 3.8 37.4 0.4
CZ A:ARG169 3.9 42.3 0.4
CZ A:ARG169 3.9 42.3 0.4
HH12 A:ARG169 3.9 38.4 0.4
HH12 A:ARG169 3.9 38.4 0.4
N A:SER104 3.9 20.6 1.0
NE A:ARG169 4.0 37.0 0.1
NE A:ARG169 4.0 37.0 0.1
HG2 A:LYS103 4.0 34.7 1.0
CZ A:ARG169 4.0 40.4 0.1
CZ A:ARG169 4.0 40.4 0.1
HH12 A:ARG169 4.0 41.0 0.1
HH12 A:ARG169 4.0 41.0 0.1
C A:SER104 4.1 19.5 1.0
C7 A:AWD401 4.2 37.4 0.1
C7 A:AWD401 4.2 37.4 0.1
H A:SER104 4.4 24.7 1.0
CG A:LYS103 4.4 28.9 1.0
HB2 A:LYS103 4.4 33.0 1.0
HG2 A:ARG169 4.4 48.7 0.4
HG2 A:ARG169 4.4 48.7 0.4
HA A:ARG105 4.4 27.8 0.1
HA A:ARG105 4.4 27.8 0.1
CG A:ARG169 4.5 40.6 0.4
CG A:ARG169 4.5 40.6 0.4
HA A:ARG105 4.5 28.1 0.4
H17 A:AWD401 4.5 34.0 0.1
H17 A:AWD401 4.5 34.0 0.1
HE A:ARG169 4.5 44.9 0.4
HE A:ARG169 4.5 44.9 0.4
HD1 A:HIS208 4.5 34.4 0.1
HD1 A:HIS208 4.5 34.4 0.1
N A:LYS103 4.6 22.4 1.0
H7 A:AWD401 4.6 22.9 0.1
H7 A:AWD401 4.6 22.9 0.1
CA A:SER104 4.6 19.7 1.0
HB3 A:ARG169 4.6 38.3 0.1
HB3 A:ARG169 4.6 38.3 0.1
HB3 A:ARG169 4.6 38.5 0.4
HB3 A:ARG169 4.6 38.5 0.4
HA A:ARG105 4.6 27.6 0.4
HE A:ARG169 4.7 44.4 0.1
HE A:ARG169 4.7 44.4 0.1
HD1 A:HIS208 4.7 34.8 0.4
HD1 A:HIS208 4.7 34.8 0.4
H A:GLY209 4.7 32.1 1.0
CG A:ARG169 4.8 34.4 0.1
CG A:ARG169 4.8 34.4 0.1
N A:ARG105 4.8 19.9 0.4
N A:ARG105 4.9 20.1 0.1
N A:ARG105 4.9 20.1 0.1
N A:ARG105 4.9 19.9 0.4
HG2 A:ARG169 4.9 41.2 0.1
HG2 A:ARG169 4.9 41.2 0.1
NH2 A:ARG169 4.9 37.5 0.4
NH2 A:ARG169 4.9 37.5 0.4
H A:LYS103 4.9 26.9 1.0
HD12 A:ILE171 5.0 33.2 0.4
HD12 A:ILE171 5.0 33.2 0.4

Reference:

D.A.Keedy, Z.B.Hill, J.T.Biel, E.Kang, T.J.Rettenmaier, J.Brandao-Neto, N.M.Pearce, F.Von Delft, J.A.Wells, J.S.Fraser. An Expanded Allosteric Network in PTP1B By Multitemperature Crystallography, Fragment Screening, and Covalent Tethering. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29877794
DOI: 10.7554/ELIFE.36307
Page generated: Sun Dec 13 12:31:41 2020

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