Fluorine in PDB 5qdv: Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000574A

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000574A:
3.1.3.48;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000574A, PDB code: 5qdv 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)	44.26 / 1.77
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.242, 90.242, 107.386, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 21.4

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000574A (pdb code 5qdv). 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_FMOPL000574A, PDB code: 5qdv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000574A


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_FMOPL000574A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:89.9 occ:0.20 F1 A:GQP401 0.0 89.9 0.2 F1 A:GQP401 0.1 91.1 0.2 C12 A:GQP401 1.4 35.1 0.2 C12 A:GQP401 1.5 35.3 0.2 HE1 A:PHE196 1.9 44.0 0.3 HD22 A:LEU195 2.0 56.8 0.2 HD22 A:LEU195 2.0 56.8 0.2 C13 A:GQP401 2.4 43.5 0.2 C11 A:GQP401 2.4 38.4 0.2 C13 A:GQP401 2.5 43.3 0.2 HD23 A:LEU195 2.5 56.8 0.2 HD23 A:LEU195 2.5 56.8 0.2 HD22 A:LEU195 2.5 30.1 0.3 HD22 A:LEU195 2.5 30.1 0.3 C11 A:GQP401 2.6 36.7 0.2 CD2 A:LEU195 2.6 47.3 0.2 CD2 A:LEU195 2.6 47.3 0.2 H6 A:GQP401 2.7 52.2 0.2 H8 A:GQP401 2.7 46.0 0.2 H6 A:GQP401 2.7 52.0 0.2 HD23 A:LEU195 2.7 30.1 0.3 HD23 A:LEU195 2.7 30.1 0.3 CE1 A:PHE196 2.7 36.7 0.3 H8 A:GQP401 2.8 44.1 0.2 HD13 A:LEU232 2.8 32.4 0.3 HD13 A:LEU232 2.8 32.4 0.3 CZ A:ARG199 2.9 37.9 0.3 CZ A:ARG199 2.9 37.9 0.3 CZ A:PHE196 2.9 41.0 0.3 HZ A:PHE196 3.0 49.2 0.3 HD1 A:PHE196 3.0 23.0 0.3 CD2 A:LEU195 3.0 25.1 0.3 CD2 A:LEU195 3.0 25.1 0.3 HG A:LEU195 3.0 33.5 0.3 HG A:LEU195 3.0 33.5 0.3 HG A:LEU195 3.0 37.0 0.2 HG A:LEU195 3.0 37.0 0.2 HD11 A:LEU232 3.0 32.4 0.3 HD11 A:LEU232 3.0 32.4 0.3 NE A:ARG199 3.1 27.3 0.3 NE A:ARG199 3.1 27.3 0.3 CZ A:ARG199 3.1 38.4 0.2 CZ A:ARG199 3.1 38.4 0.2 NH2 A:ARG199 3.1 25.8 0.3 NH2 A:ARG199 3.1 25.8 0.3 NE A:ARG199 3.2 35.5 0.2 NE A:ARG199 3.2 35.5 0.2 CE1 A:PHE196 3.2 37.1 0.3 HD2 A:ARG199 3.3 35.2 0.3 HD2 A:ARG199 3.3 35.2 0.3 CD1 A:PHE196 3.3 19.2 0.3 CE2 A:PHE196 3.3 54.5 0.3 NH1 A:ARG199 3.3 31.5 0.3 NH1 A:ARG199 3.3 31.5 0.3 NH2 A:ARG199 3.3 33.2 0.2 NH2 A:ARG199 3.3 33.2 0.2 HE A:ARG199 3.3 32.8 0.3 HE A:ARG199 3.3 32.8 0.3 HH21 A:ARG199 3.4 30.9 0.3 HH21 A:ARG199 3.4 30.9 0.3 HE A:ARG199 3.4 42.6 0.2 HE A:ARG199 3.4 42.6 0.2 HD2 A:ARG199 3.4 38.2 0.2 HD2 A:ARG199 3.4 38.2 0.2 CD1 A:LEU232 3.4 27.0 0.3 CD1 A:LEU232 3.4 27.0 0.3 CG A:LEU195 3.4 30.8 0.2 CG A:LEU195 3.4 30.8 0.2 HH21 A:ARG199 3.4 39.9 0.2 HH21 A:ARG199 3.4 39.9 0.2 HD21 A:LEU195 3.5 56.8 0.2 HD21 A:LEU195 3.5 56.8 0.2 HH22 A:ARG199 3.5 30.9 0.3 HH22 A:ARG199 3.5 30.9 0.3 HE1 A:PHE196 3.5 44.5 0.3 CG A:LEU195 3.5 27.9 0.3 CG A:LEU195 3.5 27.9 0.3 HE2 A:PHE196 3.6 65.4 0.3 HH11 A:ARG199 3.6 37.8 0.3 HH11 A:ARG199 3.6 37.8 0.3 NH1 A:ARG199 3.6 35.1 0.2 NH1 A:ARG199 3.6 35.1 0.2 HH12 A:ARG199 3.6 37.8 0.3 HH12 A:ARG199 3.6 37.8 0.3 HH22 A:ARG199 3.6 39.9 0.2 HH22 A:ARG199 3.6 39.9 0.2 HD12 A:LEU195 3.7 57.9 0.2 HD12 A:LEU195 3.7 57.9 0.2 C14 A:GQP401 3.7 52.5 0.2 C10 A:GQP401 3.7 65.7 0.2 HB2 A:LEU232 3.7 45.7 0.2 HB2 A:LEU232 3.7 45.7 0.2 CD A:ARG199 3.7 29.4 0.3 CD A:ARG199 3.7 29.4 0.3 C14 A:GQP401 3.8 52.4 0.2 HB2 A:LEU232 3.8 35.5 0.3 HB2 A:LEU232 3.8 35.5 0.3 C10 A:GQP401 3.8 66.3 0.2 HA A:ASP229 3.8 42.4 0.2 HA A:ASP229 3.8 42.4 0.2 CD A:ARG199 3.8 31.8 0.2 CD A:ARG199 3.8 31.8 0.2 CD1 A:PHE196 3.9 32.9 0.3 HD21 A:LEU195 3.9 30.1 0.3 HD21 A:LEU195 3.9 30.1 0.3 CD2 A:PHE196 3.9 41.5 0.3 HH11 A:ARG199 3.9 42.2 0.2 HH11 A:ARG199 3.9 42.2 0.2 CZ A:PHE196 3.9 50.7 0.3 HH12 A:ARG199 3.9 42.2 0.2 HH12 A:ARG199 3.9 42.2 0.2 HA A:ASP229 4.0 23.6 0.3 HA A:ASP229 4.0 23.6 0.3 HB3 A:LEU232 4.0 35.5 0.3 HB3 A:LEU232 4.0 35.5 0.3 HD12 A:LEU232 4.0 32.4 0.3 HD12 A:LEU232 4.0 32.4 0.3 HD13 A:LEU232 4.1 80.5 0.2 HD13 A:LEU232 4.1 80.5 0.2 HZ A:PHE196 4.1 60.8 0.3 CD1 A:LEU195 4.1 48.2 0.2 CD1 A:LEU195 4.1 48.2 0.2 HD12 A:LEU195 4.2 31.3 0.3 HD12 A:LEU195 4.2 31.3 0.3 HB3 A:LEU232 4.2 45.7 0.2 HB3 A:LEU232 4.2 45.7 0.2 CG A:PHE196 4.2 34.4 0.3 HB2 A:PHE196 4.2 53.4 0.2 HB2 A:PHE196 4.2 53.4 0.2 C9 A:GQP401 4.2 61.9 0.2 OD1 A:ASP229 4.2 38.4 0.2 OD1 A:ASP229 4.2 38.4 0.2 CB A:LEU232 4.3 29.6 0.3 CB A:LEU232 4.3 29.6 0.3 C9 A:GQP401 4.3 61.7 0.2 HD3 A:ARG199 4.3 35.2 0.3 HD3 A:ARG199 4.3 35.2 0.3 OD1 A:ASP229 4.4 21.8 0.3 OD1 A:ASP229 4.4 21.8 0.3 CB A:LEU232 4.4 38.1 0.2 CB A:LEU232 4.4 38.1 0.2 HD1 A:PHE196 4.4 39.4 0.3 HD3 A:ARG199 4.4 38.2 0.2 HD3 A:ARG199 4.4 38.2 0.2 CD1 A:LEU195 4.5 26.1 0.3 CD1 A:LEU195 4.5 26.1 0.3 CG A:LEU232 4.5 29.0 0.3 CG A:LEU232 4.5 29.0 0.3 HB3 A:LEU195 4.5 27.1 0.3 HB3 A:LEU195 4.5 27.1 0.3 HD2 A:PHE196 4.5 49.8 0.3 H9 A:GQP401 4.5 63.0 0.2 H5 A:GQP401 4.5 78.8 0.2 H9 A:GQP401 4.6 62.9 0.2 HG3 A:ARG199 4.6 25.7 0.3 HG3 A:ARG199 4.6 25.7 0.3 HB3 A:LEU195 4.6 47.0 0.2 HB3 A:LEU195 4.6 47.0 0.2 CG A:PHE196 4.7 20.9 0.3 CB A:LEU195 4.7 22.6 0.3 CB A:LEU195 4.7 22.6 0.3 H5 A:GQP401 4.7 79.6 0.2 CB A:LEU195 4.7 39.2 0.2 CB A:LEU195 4.7 39.2 0.2 HA A:PHE196 4.7 35.9 0.3 HD21 A:LEU232 4.7 50.3 0.2 HD21 A:LEU232 4.7 50.3 0.2 HA A:PHE196 4.7 37.0 0.3 HA A:PHE196 4.7 47.8 0.2 HA A:PHE196 4.7 47.8 0.2 HD11 A:LEU195 4.7 57.9 0.2 HD11 A:LEU195 4.7 57.9 0.2 HD11 A:ILE281 4.7 95.6 0.3 HD11 A:ILE281 4.7 95.6 0.3 HD13 A:LEU195 4.7 57.9 0.2 HD13 A:LEU195 4.7 57.9 0.2 HG3 A:ARG199 4.7 40.5 0.2 HG3 A:ARG199 4.7 40.5 0.2 CA A:ASP229 4.8 35.4 0.2 CA A:ASP229 4.8 35.4 0.2 CG A:ARG199 4.8 21.4 0.3 CG A:ARG199 4.8 21.4 0.3 O A:HOH621 4.9 37.2 1.0 CD1 A:LEU232 4.9 67.1 0.2 CD1 A:LEU232 4.9 67.1 0.2 HD21 A:LEU192 4.9 38.7 0.3 HD21 A:LEU192 4.9 38.7 0.3 CG A:LEU232 4.9 34.9 0.2 CG A:LEU232 4.9 34.9 0.2 HB2 A:ASP229 4.9 40.2 0.2 HB2 A:ASP229 4.9 40.2 0.2 CG A:ARG199 4.9 33.8 0.2 CG A:ARG199 4.9 33.8 0.2 CA A:ASP229 5.0 19.6 0.3 CA A:ASP229 5.0 19.6 0.3

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMOPL000574A


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_FMOPL000574A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:91.1 occ:0.20 F1 A:GQP401 0.0 91.1 0.2 F1 A:GQP401 0.1 89.9 0.2 C12 A:GQP401 1.3 35.1 0.2 C12 A:GQP401 1.4 35.3 0.2 HE1 A:PHE196 1.8 44.0 0.3 HD22 A:LEU195 2.2 56.8 0.2 HD22 A:LEU195 2.2 56.8 0.2 C11 A:GQP401 2.3 38.4 0.2 C13 A:GQP401 2.4 43.5 0.2 C13 A:GQP401 2.4 43.3 0.2 C11 A:GQP401 2.4 36.7 0.2 H8 A:GQP401 2.6 46.0 0.2 HD23 A:LEU195 2.6 56.8 0.2 HD23 A:LEU195 2.6 56.8 0.2 CE1 A:PHE196 2.6 36.7 0.3 HD22 A:LEU195 2.7 30.1 0.3 HD22 A:LEU195 2.7 30.1 0.3 H6 A:GQP401 2.7 52.2 0.2 H6 A:GQP401 2.7 52.0 0.2 H8 A:GQP401 2.7 44.1 0.2 CD2 A:LEU195 2.8 47.3 0.2 CD2 A:LEU195 2.8 47.3 0.2 CZ A:PHE196 2.8 41.0 0.3 HD23 A:LEU195 2.8 30.1 0.3 HD23 A:LEU195 2.8 30.1 0.3 CZ A:ARG199 2.8 37.9 0.3 CZ A:ARG199 2.8 37.9 0.3 HZ A:PHE196 2.8 49.2 0.3 HD13 A:LEU232 2.9 32.4 0.3 HD13 A:LEU232 2.9 32.4 0.3 HD1 A:PHE196 2.9 23.0 0.3 HG A:LEU195 3.1 37.0 0.2 HG A:LEU195 3.1 37.0 0.2 HG A:LEU195 3.1 33.5 0.3 HG A:LEU195 3.1 33.5 0.3 CZ A:ARG199 3.1 38.4 0.2 CZ A:ARG199 3.1 38.4 0.2 NE A:ARG199 3.1 27.3 0.3 NE A:ARG199 3.1 27.3 0.3 CE1 A:PHE196 3.1 37.1 0.3 CD2 A:LEU195 3.1 25.1 0.3 CD2 A:LEU195 3.1 25.1 0.3 HD11 A:LEU232 3.1 32.4 0.3 HD11 A:LEU232 3.1 32.4 0.3 NH2 A:ARG199 3.2 25.8 0.3 NH2 A:ARG199 3.2 25.8 0.3 CD1 A:PHE196 3.2 19.2 0.3 NE A:ARG199 3.2 35.5 0.2 NE A:ARG199 3.2 35.5 0.2 CE2 A:PHE196 3.2 54.5 0.3 HD2 A:ARG199 3.2 35.2 0.3 HD2 A:ARG199 3.2 35.2 0.3 NH1 A:ARG199 3.2 31.5 0.3 NH1 A:ARG199 3.2 31.5 0.3 NH2 A:ARG199 3.3 33.2 0.2 NH2 A:ARG199 3.3 33.2 0.2 HD2 A:ARG199 3.3 38.2 0.2 HD2 A:ARG199 3.3 38.2 0.2 HE A:ARG199 3.4 32.8 0.3 HE A:ARG199 3.4 32.8 0.3 HE1 A:PHE196 3.4 44.5 0.3 HE A:ARG199 3.4 42.6 0.2 HE A:ARG199 3.4 42.6 0.2 HH21 A:ARG199 3.4 30.9 0.3 HH21 A:ARG199 3.4 30.9 0.3 CD1 A:LEU232 3.5 27.0 0.3 CD1 A:LEU232 3.5 27.0 0.3 CG A:LEU195 3.5 30.8 0.2 CG A:LEU195 3.5 30.8 0.2 HH11 A:ARG199 3.5 37.8 0.3 HH11 A:ARG199 3.5 37.8 0.3 HH21 A:ARG199 3.5 39.9 0.2 HH21 A:ARG199 3.5 39.9 0.2 HH22 A:ARG199 3.5 30.9 0.3 HH22 A:ARG199 3.5 30.9 0.3 HE2 A:PHE196 3.5 65.4 0.3 NH1 A:ARG199 3.5 35.1 0.2 NH1 A:ARG199 3.5 35.1 0.2 HH12 A:ARG199 3.5 37.8 0.3 HH12 A:ARG199 3.5 37.8 0.3 C10 A:GQP401 3.6 65.7 0.2 HD21 A:LEU195 3.6 56.8 0.2 HD21 A:LEU195 3.6 56.8 0.2 C14 A:GQP401 3.6 52.5 0.2 CG A:LEU195 3.6 27.9 0.3 CG A:LEU195 3.6 27.9 0.3 HH22 A:ARG199 3.7 39.9 0.2 HH22 A:ARG199 3.7 39.9 0.2 C14 A:GQP401 3.7 52.4 0.2 C10 A:GQP401 3.7 66.3 0.2 CD A:ARG199 3.7 29.4 0.3 CD A:ARG199 3.7 29.4 0.3 CD1 A:PHE196 3.7 32.9 0.3 HB2 A:LEU232 3.8 45.7 0.2 HB2 A:LEU232 3.8 45.7 0.2 HD12 A:LEU195 3.8 57.9 0.2 HD12 A:LEU195 3.8 57.9 0.2 CD A:ARG199 3.8 31.8 0.2 CD A:ARG199 3.8 31.8 0.2 HH11 A:ARG199 3.8 42.2 0.2 HH11 A:ARG199 3.8 42.2 0.2 CD2 A:PHE196 3.8 41.5 0.3 CZ A:PHE196 3.8 50.7 0.3 HB2 A:LEU232 3.9 35.5 0.3 HB2 A:LEU232 3.9 35.5 0.3 HH12 A:ARG199 3.9 42.2 0.2 HH12 A:ARG199 3.9 42.2 0.2 HA A:ASP229 4.0 42.4 0.2 HA A:ASP229 4.0 42.4 0.2 HD21 A:LEU195 4.0 30.1 0.3 HD21 A:LEU195 4.0 30.1 0.3 HZ A:PHE196 4.0 60.8 0.3 HB3 A:LEU232 4.0 35.5 0.3 HB3 A:LEU232 4.0 35.5 0.3 CG A:PHE196 4.1 34.4 0.3 HD12 A:LEU232 4.1 32.4 0.3 HD12 A:LEU232 4.1 32.4 0.3 HB2 A:PHE196 4.1 53.4 0.2 HB2 A:PHE196 4.1 53.4 0.2 C9 A:GQP401 4.1 61.9 0.2 HA A:ASP229 4.1 23.6 0.3 HA A:ASP229 4.1 23.6 0.3 HD13 A:LEU232 4.2 80.5 0.2 HD13 A:LEU232 4.2 80.5 0.2 HB3 A:LEU232 4.2 45.7 0.2 HB3 A:LEU232 4.2 45.7 0.2 CD1 A:LEU195 4.2 48.2 0.2 CD1 A:LEU195 4.2 48.2 0.2 C9 A:GQP401 4.2 61.7 0.2 HD12 A:LEU195 4.2 31.3 0.3 HD12 A:LEU195 4.2 31.3 0.3 HD3 A:ARG199 4.3 35.2 0.3 HD3 A:ARG199 4.3 35.2 0.3 OD1 A:ASP229 4.3 38.4 0.2 OD1 A:ASP229 4.3 38.4 0.2 HD1 A:PHE196 4.3 39.4 0.3 CB A:LEU232 4.3 29.6 0.3 CB A:LEU232 4.3 29.6 0.3 HD3 A:ARG199 4.4 38.2 0.2 HD3 A:ARG199 4.4 38.2 0.2 CB A:LEU232 4.4 38.1 0.2 CB A:LEU232 4.4 38.1 0.2 H5 A:GQP401 4.4 78.8 0.2 HD2 A:PHE196 4.4 49.8 0.3 OD1 A:ASP229 4.4 21.8 0.3 OD1 A:ASP229 4.4 21.8 0.3 H9 A:GQP401 4.5 63.0 0.2 CG A:LEU232 4.5 29.0 0.3 CG A:LEU232 4.5 29.0 0.3 H9 A:GQP401 4.5 62.9 0.2 H5 A:GQP401 4.5 79.6 0.2 HB3 A:LEU195 4.5 27.1 0.3 HB3 A:LEU195 4.5 27.1 0.3 CD1 A:LEU195 4.5 26.1 0.3 CD1 A:LEU195 4.5 26.1 0.3 CG A:PHE196 4.6 20.9 0.3 HA A:PHE196 4.6 35.9 0.3 HD11 A:ILE281 4.6 95.6 0.3 HD11 A:ILE281 4.6 95.6 0.3 HG3 A:ARG199 4.6 25.7 0.3 HG3 A:ARG199 4.6 25.7 0.3 HA A:PHE196 4.6 37.0 0.3 HA A:PHE196 4.6 47.8 0.2 HA A:PHE196 4.6 47.8 0.2 HB3 A:LEU195 4.7 47.0 0.2 HB3 A:LEU195 4.7 47.0 0.2 HD21 A:LEU232 4.7 50.3 0.2 HD21 A:LEU232 4.7 50.3 0.2 HG3 A:ARG199 4.7 40.5 0.2 HG3 A:ARG199 4.7 40.5 0.2 CB A:LEU195 4.7 22.6 0.3 CB A:LEU195 4.7 22.6 0.3 CB A:LEU195 4.7 39.2 0.2 CB A:LEU195 4.7 39.2 0.2 HD11 A:LEU195 4.8 57.9 0.2 HD11 A:LEU195 4.8 57.9 0.2 CG A:ARG199 4.8 21.4 0.3 CG A:ARG199 4.8 21.4 0.3 O A:HOH621 4.8 37.2 1.0 HD13 A:LEU195 4.8 57.9 0.2 HD13 A:LEU195 4.8 57.9 0.2 CG A:ARG199 4.9 33.8 0.2 CG A:ARG199 4.9 33.8 0.2 HD21 A:LEU192 4.9 38.7 0.3 HD21 A:LEU192 4.9 38.7 0.3 CA A:ASP229 4.9 35.4 0.2 CA A:ASP229 4.9 35.4 0.2 CB A:PHE196 4.9 44.5 0.2 CB A:PHE196 4.9 44.5 0.2 CD1 A:LEU232 5.0 67.1 0.2 CD1 A:LEU232 5.0 67.1 0.2 CG A:LEU232 5.0 34.9 0.2 CG A:LEU232 5.0 34.9 0.2

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