Fluorine in PDB 5qfo: Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_XST00000644B

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_XST00000644B:
3.1.3.48;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_XST00000644B, PDB code: 5qfo 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)	62.95 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.072, 90.072, 106.610, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 21.9

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_XST00000644B (pdb code 5qfo). 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_XST00000644B, PDB code: 5qfo:
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_XST00000644B


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_XST00000644B within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:20.0 occ:0.21 FAG A:8H8401 0.0 20.0 0.2 FAG A:8H8401 0.0 20.0 0.2 CAF A:8H8401 1.3 25.5 0.2 CAF A:8H8401 1.3 25.5 0.2 CAB A:8H8401 2.3 22.2 0.2 CAB A:8H8401 2.3 22.2 0.2 CAI A:8H8401 2.3 15.8 0.2 CAI A:8H8401 2.3 15.8 0.2 H1 A:8H8401 2.5 19.0 0.2 H1 A:8H8401 2.5 19.0 0.2 HG2 A:GLU252 2.6 31.4 0.3 HG2 A:GLU252 2.6 31.4 0.3 CAC A:8H8401 2.7 26.4 0.2 CAC A:8H8401 2.7 26.4 0.2 HA A:VAL249 2.7 32.3 0.3 HA A:VAL249 2.7 32.3 0.3 HA A:VAL249 2.7 32.8 0.2 HA A:VAL249 2.7 32.8 0.2 HE2 A:MET74 2.7 35.4 0.3 HE2 A:MET74 2.7 35.4 0.3 HB3 A:GLU252 2.7 29.1 0.3 HB3 A:GLU252 2.7 29.1 0.3 HB3 A:GLU252 2.8 38.5 0.2 HB3 A:GLU252 2.8 38.5 0.2 HE3 A:MET74 2.9 35.4 0.3 HE3 A:MET74 2.9 35.4 0.3 HG2 A:GLU252 3.0 50.8 0.2 HG2 A:GLU252 3.0 50.8 0.2 HE3 A:MET74 3.0 48.5 0.2 HE3 A:MET74 3.0 48.5 0.2 HG13 A:VAL249 3.1 30.0 0.3 HG13 A:VAL249 3.1 30.0 0.3 CE A:MET74 3.2 29.5 0.3 CE A:MET74 3.2 29.5 0.3 HG21 A:VAL249 3.2 34.6 0.3 HG21 A:VAL249 3.2 34.6 0.3 HE2 A:MET74 3.3 48.5 0.2 HE2 A:MET74 3.3 48.5 0.2 HB2 A:GLU252 3.3 29.1 0.3 HB2 A:GLU252 3.3 29.1 0.3 CB A:GLU252 3.3 24.2 0.3 CB A:GLU252 3.3 24.2 0.3 HG13 A:VAL249 3.3 38.2 0.2 HG13 A:VAL249 3.3 38.2 0.2 CG A:GLU252 3.3 26.1 0.3 CG A:GLU252 3.3 26.1 0.3 NAD A:8H8401 3.4 15.4 0.2 NAD A:8H8401 3.4 15.4 0.2 HE1 A:MET74 3.4 35.4 0.3 HE1 A:MET74 3.4 35.4 0.3 CB A:GLU252 3.5 32.1 0.2 CB A:GLU252 3.5 32.1 0.2 CE A:MET74 3.6 40.4 0.2 CE A:MET74 3.6 40.4 0.2 CAH A:8H8401 3.6 28.7 0.2 CAH A:8H8401 3.6 28.7 0.2 CAA A:8H8401 3.6 22.4 0.2 CAA A:8H8401 3.6 22.4 0.2 HG21 A:VAL249 3.6 57.1 0.2 HG21 A:VAL249 3.6 57.1 0.2 HB2 A:GLU252 3.6 38.5 0.2 HB2 A:GLU252 3.6 38.5 0.2 CA A:VAL249 3.6 26.9 0.3 CA A:VAL249 3.6 26.9 0.3 CA A:VAL249 3.7 27.4 0.2 CA A:VAL249 3.7 27.4 0.2 CG A:GLU252 3.7 42.4 0.2 CG A:GLU252 3.7 42.4 0.2 HG3 A:GLU252 3.8 31.4 0.3 HG3 A:GLU252 3.8 31.4 0.3 HE1 A:MET74 3.9 48.5 0.2 HE1 A:MET74 3.9 48.5 0.2 CG1 A:VAL249 3.9 25.0 0.3 CG1 A:VAL249 3.9 25.0 0.3 CG2 A:VAL249 4.0 28.9 0.3 CG2 A:VAL249 4.0 28.9 0.3 CAE A:8H8401 4.0 24.9 0.2 CAE A:8H8401 4.0 24.9 0.2 CB A:VAL249 4.0 28.4 0.3 CB A:VAL249 4.0 28.4 0.3 O A:VAL249 4.1 24.4 0.3 O A:VAL249 4.1 24.4 0.3 O A:VAL249 4.1 37.1 0.2 O A:VAL249 4.1 37.1 0.2 CG1 A:VAL249 4.1 31.8 0.2 CG1 A:VAL249 4.1 31.8 0.2 HG3 A:GLU252 4.2 50.8 0.2 HG3 A:GLU252 4.2 50.8 0.2 CB A:VAL249 4.2 33.9 0.2 CB A:VAL249 4.2 33.9 0.2 O A:LYS248 4.2 38.2 0.2 O A:LYS248 4.2 38.2 0.2 HD12 A:LEU234 4.3 60.4 0.2 HD12 A:LEU234 4.3 60.4 0.2 HD12 A:LEU234 4.3 30.5 0.3 HD12 A:LEU234 4.3 30.5 0.3 CG2 A:VAL249 4.3 47.6 0.2 CG2 A:VAL249 4.3 47.6 0.2 C A:VAL249 4.4 22.0 0.3 C A:VAL249 4.4 22.0 0.3 HG11 A:VAL249 4.4 30.0 0.3 HG11 A:VAL249 4.4 30.0 0.3 C A:VAL249 4.4 22.6 0.2 C A:VAL249 4.4 22.6 0.2 H4 A:8H8401 4.4 26.9 0.2 H4 A:8H8401 4.4 26.9 0.2 O A:LYS248 4.4 26.1 0.3 O A:LYS248 4.4 26.1 0.3 HG22 A:THR230 4.5 35.0 1.0 N A:VAL249 4.5 31.7 0.2 N A:VAL249 4.5 31.7 0.2 HG11 A:VAL249 4.5 38.2 0.2 HG11 A:VAL249 4.5 38.2 0.2 CD A:GLU252 4.5 34.6 0.3 CD A:GLU252 4.5 34.6 0.3 HG23 A:VAL249 4.5 34.6 0.3 HG23 A:VAL249 4.5 34.6 0.3 HG12 A:VAL249 4.5 30.0 0.3 HG12 A:VAL249 4.5 30.0 0.3 N A:VAL249 4.6 30.3 0.3 N A:VAL249 4.6 30.3 0.3 HB3 A:MET74 4.6 36.5 0.2 HB3 A:MET74 4.6 36.5 0.2 H2 A:8H8401 4.6 31.0 0.2 H2 A:8H8401 4.6 31.0 0.2 HG22 A:VAL249 4.6 34.6 0.3 HG22 A:VAL249 4.6 34.6 0.3 H A:GLU252 4.6 32.3 0.2 H A:GLU252 4.6 32.3 0.2 C A:LYS248 4.7 26.1 0.2 C A:LYS248 4.7 26.1 0.2 HD13 A:LEU234 4.7 60.4 0.2 HD13 A:LEU234 4.7 60.4 0.2 OAJ A:8H8401 4.7 25.8 0.2 OAJ A:8H8401 4.7 25.8 0.2 CA A:GLU252 4.8 23.3 0.3 CA A:GLU252 4.8 23.3 0.3 HG12 A:VAL249 4.8 38.2 0.2 HG12 A:VAL249 4.8 38.2 0.2 SD A:MET74 4.8 25.1 0.3 SD A:MET74 4.8 25.1 0.3 CD A:GLU252 4.8 42.8 0.2 CD A:GLU252 4.8 42.8 0.2 H A:GLU252 4.8 34.6 0.3 H A:GLU252 4.8 34.6 0.3 HG23 A:VAL249 4.8 57.1 0.2 HG23 A:VAL249 4.8 57.1 0.2 CD1 A:LEU234 4.8 50.4 0.2 CD1 A:LEU234 4.8 50.4 0.2 HG3 A:MET253 4.9 42.3 0.3 HG3 A:MET253 4.9 42.3 0.3 H A:MET253 4.9 30.5 0.3 H A:MET253 4.9 30.5 0.3 CA A:GLU252 4.9 25.7 0.2 CA A:GLU252 4.9 25.7 0.2 HG3 A:MET253 4.9 43.6 0.2 HG3 A:MET253 4.9 43.6 0.2 HB3 A:MET74 4.9 30.4 0.3 HB3 A:MET74 4.9 30.4 0.3 C A:LYS248 4.9 24.0 0.3 C A:LYS248 4.9 24.0 0.3 H A:MET253 4.9 43.1 0.2 H A:MET253 4.9 43.1 0.2 O A:HOH556 4.9 63.1 1.0 HD11 A:LEU234 4.9 60.4 0.2 HD11 A:LEU234 4.9 60.4 0.2 HG22 A:VAL249 5.0 57.1 0.2 HG22 A:VAL249 5.0 57.1 0.2 OE1 A:GLU252 5.0 26.7 0.3 OE1 A:GLU252 5.0 26.7 0.3

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_XST00000644B


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_XST00000644B within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:20.0 occ:0.21 FAG A:8H8401 0.0 20.0 0.2 FAG A:8H8401 0.0 20.0 0.2 CAF A:8H8401 1.3 25.5 0.2 CAF A:8H8401 1.3 25.5 0.2 CAB A:8H8401 2.3 22.2 0.2 CAB A:8H8401 2.3 22.2 0.2 CAI A:8H8401 2.3 15.8 0.2 CAI A:8H8401 2.3 15.8 0.2 H1 A:8H8401 2.5 19.0 0.2 H1 A:8H8401 2.5 19.0 0.2 HG2 A:GLU252 2.6 31.4 0.3 HG2 A:GLU252 2.6 31.4 0.3 CAC A:8H8401 2.7 26.4 0.2 CAC A:8H8401 2.7 26.4 0.2 HA A:VAL249 2.7 32.3 0.3 HA A:VAL249 2.7 32.3 0.3 HA A:VAL249 2.7 32.8 0.2 HA A:VAL249 2.7 32.8 0.2 HE2 A:MET74 2.7 35.4 0.3 HE2 A:MET74 2.7 35.4 0.3 HB3 A:GLU252 2.7 29.1 0.3 HB3 A:GLU252 2.7 29.1 0.3 HB3 A:GLU252 2.8 38.5 0.2 HB3 A:GLU252 2.8 38.5 0.2 HE3 A:MET74 2.9 35.4 0.3 HE3 A:MET74 2.9 35.4 0.3 HG2 A:GLU252 3.0 50.8 0.2 HG2 A:GLU252 3.0 50.8 0.2 HE3 A:MET74 3.0 48.5 0.2 HE3 A:MET74 3.0 48.5 0.2 HG13 A:VAL249 3.1 30.0 0.3 HG13 A:VAL249 3.1 30.0 0.3 CE A:MET74 3.2 29.5 0.3 CE A:MET74 3.2 29.5 0.3 HG21 A:VAL249 3.2 34.6 0.3 HG21 A:VAL249 3.2 34.6 0.3 HE2 A:MET74 3.3 48.5 0.2 HE2 A:MET74 3.3 48.5 0.2 HB2 A:GLU252 3.3 29.1 0.3 HB2 A:GLU252 3.3 29.1 0.3 CB A:GLU252 3.3 24.2 0.3 CB A:GLU252 3.3 24.2 0.3 HG13 A:VAL249 3.3 38.2 0.2 HG13 A:VAL249 3.3 38.2 0.2 CG A:GLU252 3.3 26.1 0.3 CG A:GLU252 3.3 26.1 0.3 NAD A:8H8401 3.4 15.4 0.2 NAD A:8H8401 3.4 15.4 0.2 HE1 A:MET74 3.4 35.4 0.3 HE1 A:MET74 3.4 35.4 0.3 CB A:GLU252 3.5 32.1 0.2 CB A:GLU252 3.5 32.1 0.2 CE A:MET74 3.6 40.4 0.2 CE A:MET74 3.6 40.4 0.2 CAH A:8H8401 3.6 28.7 0.2 CAH A:8H8401 3.6 28.7 0.2 CAA A:8H8401 3.6 22.4 0.2 CAA A:8H8401 3.6 22.4 0.2 HG21 A:VAL249 3.6 57.1 0.2 HG21 A:VAL249 3.6 57.1 0.2 HB2 A:GLU252 3.6 38.5 0.2 HB2 A:GLU252 3.6 38.5 0.2 CA A:VAL249 3.6 26.9 0.3 CA A:VAL249 3.6 26.9 0.3 CA A:VAL249 3.7 27.4 0.2 CA A:VAL249 3.7 27.4 0.2 CG A:GLU252 3.7 42.4 0.2 CG A:GLU252 3.7 42.4 0.2 HG3 A:GLU252 3.8 31.4 0.3 HG3 A:GLU252 3.8 31.4 0.3 HE1 A:MET74 3.9 48.5 0.2 HE1 A:MET74 3.9 48.5 0.2 CG1 A:VAL249 3.9 25.0 0.3 CG1 A:VAL249 3.9 25.0 0.3 CG2 A:VAL249 4.0 28.9 0.3 CG2 A:VAL249 4.0 28.9 0.3 CAE A:8H8401 4.0 24.9 0.2 CAE A:8H8401 4.0 24.9 0.2 CB A:VAL249 4.0 28.4 0.3 CB A:VAL249 4.0 28.4 0.3 O A:VAL249 4.1 24.4 0.3 O A:VAL249 4.1 24.4 0.3 O A:VAL249 4.1 37.1 0.2 O A:VAL249 4.1 37.1 0.2 CG1 A:VAL249 4.1 31.8 0.2 CG1 A:VAL249 4.1 31.8 0.2 HG3 A:GLU252 4.2 50.8 0.2 HG3 A:GLU252 4.2 50.8 0.2 CB A:VAL249 4.2 33.9 0.2 CB A:VAL249 4.2 33.9 0.2 O A:LYS248 4.2 38.2 0.2 O A:LYS248 4.2 38.2 0.2 HD12 A:LEU234 4.3 60.4 0.2 HD12 A:LEU234 4.3 60.4 0.2 HD12 A:LEU234 4.3 30.5 0.3 HD12 A:LEU234 4.3 30.5 0.3 CG2 A:VAL249 4.3 47.6 0.2 CG2 A:VAL249 4.3 47.6 0.2 C A:VAL249 4.4 22.0 0.3 C A:VAL249 4.4 22.0 0.3 HG11 A:VAL249 4.4 30.0 0.3 HG11 A:VAL249 4.4 30.0 0.3 C A:VAL249 4.4 22.6 0.2 C A:VAL249 4.4 22.6 0.2 H4 A:8H8401 4.4 26.9 0.2 H4 A:8H8401 4.4 26.9 0.2 O A:LYS248 4.4 26.1 0.3 O A:LYS248 4.4 26.1 0.3 HG22 A:THR230 4.5 35.0 1.0 N A:VAL249 4.5 31.7 0.2 N A:VAL249 4.5 31.7 0.2 HG11 A:VAL249 4.5 38.2 0.2 HG11 A:VAL249 4.5 38.2 0.2 CD A:GLU252 4.5 34.6 0.3 CD A:GLU252 4.5 34.6 0.3 HG23 A:VAL249 4.5 34.6 0.3 HG23 A:VAL249 4.5 34.6 0.3 HG12 A:VAL249 4.5 30.0 0.3 HG12 A:VAL249 4.5 30.0 0.3 N A:VAL249 4.6 30.3 0.3 N A:VAL249 4.6 30.3 0.3 HB3 A:MET74 4.6 36.5 0.2 HB3 A:MET74 4.6 36.5 0.2 H2 A:8H8401 4.6 31.0 0.2 H2 A:8H8401 4.6 31.0 0.2 HG22 A:VAL249 4.6 34.6 0.3 HG22 A:VAL249 4.6 34.6 0.3 H A:GLU252 4.6 32.3 0.2 H A:GLU252 4.6 32.3 0.2 C A:LYS248 4.7 26.1 0.2 C A:LYS248 4.7 26.1 0.2 HD13 A:LEU234 4.7 60.4 0.2 HD13 A:LEU234 4.7 60.4 0.2 OAJ A:8H8401 4.7 25.8 0.2 OAJ A:8H8401 4.7 25.8 0.2 CA A:GLU252 4.8 23.3 0.3 CA A:GLU252 4.8 23.3 0.3 HG12 A:VAL249 4.8 38.2 0.2 HG12 A:VAL249 4.8 38.2 0.2 SD A:MET74 4.8 25.1 0.3 SD A:MET74 4.8 25.1 0.3 CD A:GLU252 4.8 42.8 0.2 CD A:GLU252 4.8 42.8 0.2 H A:GLU252 4.8 34.6 0.3 H A:GLU252 4.8 34.6 0.3 HG23 A:VAL249 4.8 57.1 0.2 HG23 A:VAL249 4.8 57.1 0.2 CD1 A:LEU234 4.8 50.4 0.2 CD1 A:LEU234 4.8 50.4 0.2 HG3 A:MET253 4.9 42.3 0.3 HG3 A:MET253 4.9 42.3 0.3 H A:MET253 4.9 30.5 0.3 H A:MET253 4.9 30.5 0.3 CA A:GLU252 4.9 25.7 0.2 CA A:GLU252 4.9 25.7 0.2 HG3 A:MET253 4.9 43.6 0.2 HG3 A:MET253 4.9 43.6 0.2 HB3 A:MET74 4.9 30.4 0.3 HB3 A:MET74 4.9 30.4 0.3 C A:LYS248 4.9 24.0 0.3 C A:LYS248 4.9 24.0 0.3 H A:MET253 4.9 43.1 0.2 H A:MET253 4.9 43.1 0.2 O A:HOH556 4.9 63.1 1.0 HD11 A:LEU234 4.9 60.4 0.2 HD11 A:LEU234 4.9 60.4 0.2 HG22 A:VAL249 5.0 57.1 0.2 HG22 A:VAL249 5.0 57.1 0.2 OE1 A:GLU252 5.0 26.7 0.3 OE1 A:GLU252 5.0 26.7 0.3

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