Bromine in PDB 8xbk: Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor

The structure of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor, PDB code: 8xbk was solved by H.Cao, X.Zhang, Y.Ren, J.Wan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.115, 82.95, 275.921, 90, 90, 90
R / Rfree (%)	18.3 / 23.4

The structure of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Bromine atom in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor (pdb code 8xbk). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor, PDB code: 8xbk:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:116.5 occ:1.00 BR1 A:YR9401 0.0 116.5 1.0 C24 A:YR9401 1.9 76.5 1.0 C26 A:YR9401 2.8 68.4 1.0 C23 A:YR9401 2.9 66.0 1.0 O C:THR27 3.5 56.6 1.0 C20 A:YR9401 4.1 63.1 1.0 C C:THR27 4.1 55.7 1.0 C22 C:YR9401 4.2 66.3 1.0 C22 A:YR9401 4.2 64.8 1.0 C21 C:YR9401 4.4 55.1 1.0 CA C:THR27 4.5 51.2 1.0 CA A:ARG22 4.5 58.5 1.0 CG A:ARG22 4.6 61.0 1.0 CB A:ARG22 4.7 60.7 1.0 O C:GLY26 4.7 54.1 1.0 C21 A:YR9401 4.7 62.4 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:87.4 occ:1.00 BR1 B:YR9401 0.0 87.4 1.0 C24 B:YR9401 1.9 72.2 1.0 C23 B:YR9401 2.9 71.8 1.0 C26 B:YR9401 2.9 61.4 1.0 CG B:MET18 3.3 51.0 1.0 SD D:MET18 3.7 69.4 1.0 CE D:MET18 3.7 42.8 1.0 SD B:MET18 4.0 63.9 1.0 N19 D:YR9401 4.1 63.3 1.0 C22 B:YR9401 4.2 73.9 1.0 C20 B:YR9401 4.2 61.5 1.0 CA D:GLY28 4.2 52.5 1.0 CD B:ARG22 4.3 59.4 1.0 CG B:ARG22 4.3 55.6 1.0 C20 D:YR9401 4.3 63.3 1.0 C21 D:YR9401 4.4 63.4 1.0 O D:GLY28 4.5 47.0 1.0 CG2 D:THR31 4.5 41.4 1.0 CB B:MET18 4.6 44.4 1.0 CB D:THR31 4.7 41.3 1.0 C21 B:YR9401 4.7 66.5 1.0 O B:MET18 4.8 47.5 1.0 CE B:MET18 4.9 54.5 1.0 C D:GLY28 4.9 43.8 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Br401 b:83.7 occ:1.00 BR1 C:YR9401 0.0 83.7 1.0 C24 C:YR9401 1.9 72.8 1.0 C23 C:YR9401 2.8 70.3 1.0 C26 C:YR9401 3.0 64.5 1.0 CG C:MET18 3.4 51.5 1.0 O C:HOH553 3.5 57.0 1.0 SD C:MET18 3.7 65.1 1.0 C22 C:YR9401 4.1 66.3 1.0 C21 A:YR9401 4.1 62.4 1.0 CA A:GLY28 4.1 44.8 1.0 CG2 A:THR31 4.2 34.9 1.0 C20 C:YR9401 4.2 63.3 1.0 O A:GLY28 4.3 45.0 1.0 CD C:ARG22 4.3 59.6 1.0 CG A:MET18 4.4 61.1 1.0 CB A:THR31 4.4 41.9 1.0 CG C:ARG22 4.4 60.6 1.0 C22 A:YR9401 4.4 64.8 1.0 SD A:MET18 4.4 70.1 1.0 C21 C:YR9401 4.6 55.1 1.0 C A:GLY28 4.7 45.0 1.0 O18 A:YR9401 4.7 51.6 1.0 C20 A:YR9401 4.8 63.1 1.0 CB C:MET18 4.8 41.7 1.0 OG1 A:THR31 4.8 44.4 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Br401 b:100.9 occ:1.00 BR1 D:YR9401 0.0 100.9 1.0 C24 D:YR9401 1.9 72.8 1.0 C23 D:YR9401 2.8 62.8 1.0 C26 D:YR9401 3.0 67.2 1.0 O B:THR27 3.8 46.3 1.0 C21 B:YR9401 4.1 66.5 1.0 C22 D:YR9401 4.1 65.0 1.0 C20 D:YR9401 4.2 63.3 1.0 O B:GLY26 4.3 48.9 1.0 C B:THR27 4.3 44.6 1.0 C22 B:YR9401 4.3 73.9 1.0 CA B:THR27 4.5 48.8 1.0 C21 D:YR9401 4.7 63.4 1.0 C20 B:YR9401 4.7 61.5 1.0

H.Cao, Z.Huang, Z.Liu, X.Zhang, Y.Ren, M.S.Hameed, L.Rao, N.P.Makunga, G.M.Dobrikov, J.Wan. Structure-Guided Design of Affinity/Covalent-Bond Dual-Driven Inhibitors Targeting the Amp Site of Fbpase J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.4C01886