Fluorine in PDB 7erb: Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc)

All present enzymatic activity of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc):
1.3.1.24; 1.5.1.30;

The structure of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc), PDB code: 7erb was solved by C.Griesinger, D.Lee, K.S.Ryu, M.Kim, J.H.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.71 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.423, 117.338, 82.045, 90, 90, 90
R / Rfree (%)	17.1 / 19.9

The binding sites of Fluorine atom in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc) (pdb code 7erb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc), PDB code: 7erb:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc) within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:29.1 occ:1.00 F01 A:JBF402 0.0 29.1 1.0 C02 A:JBF402 1.4 27.3 1.0 C07 A:JBF402 2.3 25.1 1.0 C03 A:JBF402 2.4 27.1 1.0 O A:HOH607 2.5 18.4 1.0 N09 A:JBF402 2.6 20.3 1.0 C08 A:JBF402 2.7 21.5 1.0 C06 A:JBF402 3.6 25.7 1.0 C2N A:NAP401 3.6 7.6 1.0 C04 A:JBF402 3.6 26.4 1.0 O2D A:NAP401 3.7 9.0 1.0 C3N A:NAP401 3.8 9.0 1.0 N1N A:NAP401 3.8 7.3 1.0 C10 A:JBF402 4.0 19.9 1.0 O21 A:JBF402 4.1 21.1 1.0 C05 A:JBF402 4.1 26.0 1.0 O A:HOH577 4.1 17.7 1.0 C4N A:NAP401 4.2 8.9 1.0 C6N A:NAP401 4.2 8.1 1.0 CD2 A:LEU125 4.3 17.8 1.0 C5N A:NAP401 4.3 8.4 1.0 C7N A:NAP401 4.4 10.0 1.0 C2D A:NAP401 4.4 7.6 1.0 C1D A:NAP401 4.5 7.5 1.0 N20 A:JBF402 4.6 20.8 1.0 CG1 A:VAL128 4.6 11.9 1.0 O7N A:NAP401 4.7 11.9 1.0 CE1 A:HIS132 4.7 7.3 1.0 CD1 A:LEU125 4.8 17.0 1.0 C19 A:JBF402 4.8 16.1 1.0 CE2 A:PHE113 4.9 11.6 1.0 C11 A:JBF402 4.9 17.4 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:57.4 occ:1.00 F01 A:JBF403 0.0 57.4 1.0 C02 A:JBF403 1.4 57.2 1.0 C07 A:JBF403 2.4 55.2 1.0 C03 A:JBF403 2.4 58.1 1.0 O B:HOH525 2.5 31.2 1.0 N09 A:JBF403 2.6 51.2 1.0 C08 A:JBF403 2.8 51.8 1.0 NH1 A:ARG134 3.0 12.5 1.0 CD A:ARG134 3.3 11.3 1.0 CG A:ARG134 3.3 9.4 1.0 ND1 B:HIS153 3.4 18.1 1.0 C04 A:JBF403 3.7 57.9 1.0 C06 A:JBF403 3.7 56.2 1.0 CB B:HIS153 3.8 17.8 1.0 C10 A:JBF403 3.8 50.4 1.0 CZ A:ARG134 3.9 11.7 1.0 NE A:ARG134 4.0 10.8 1.0 CA B:HIS153 4.0 16.8 1.0 CG B:HIS153 4.1 18.3 1.0 C05 A:JBF403 4.1 57.2 1.0 O21 A:JBF403 4.1 51.2 1.0 C12 A:JBF403 4.4 45.1 1.0 CE1 B:HIS153 4.5 18.7 1.0 O7N B:NAP401 4.5 19.7 1.0 N B:HIS153 4.5 18.0 1.0 O A:ASP130 4.6 8.5 1.0 N20 A:JBF403 4.6 51.0 1.0 C11 A:JBF403 4.7 46.6 1.0 O B:HOH668 4.7 47.5 1.0 O A:HOH611 4.8 18.3 1.0 CB A:ARG134 4.8 8.1 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc) within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:24.1 occ:1.00 F01 C:JBF402 0.0 24.1 1.0 C02 C:JBF402 1.3 21.6 1.0 C07 C:JBF402 2.3 19.3 1.0 C03 C:JBF402 2.4 20.6 1.0 O C:HOH619 2.5 16.6 1.0 N09 C:JBF402 2.7 17.5 1.0 C08 C:JBF402 2.7 18.3 1.0 C2N C:NAP401 3.4 8.7 1.0 O2D C:NAP401 3.5 7.7 1.0 C06 C:JBF402 3.5 19.5 1.0 C04 C:JBF402 3.6 19.8 1.0 C3N C:NAP401 3.6 8.7 1.0 N1N C:NAP401 3.7 7.5 1.0 C05 C:JBF402 4.0 19.4 1.0 O21 C:JBF402 4.1 18.7 1.0 C10 C:JBF402 4.1 17.5 1.0 C6N C:NAP401 4.1 8.5 1.0 C4N C:NAP401 4.1 9.1 1.0 C7N C:NAP401 4.2 10.2 1.0 O C:HOH578 4.2 16.9 1.0 C2D C:NAP401 4.2 7.1 1.0 C1D C:NAP401 4.3 7.6 1.0 CD2 C:LEU125 4.3 16.4 1.0 C5N C:NAP401 4.4 8.0 1.0 O7N C:NAP401 4.4 13.4 1.0 CG1 C:VAL128 4.6 12.0 1.0 CE1 C:HIS132 4.7 7.9 1.0 N20 C:JBF402 4.7 17.6 1.0 O C:HOH540 4.8 9.5 1.0 CD1 C:LEU125 4.9 16.3 1.0 N7N C:NAP401 5.0 8.7 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Ataluren (Ptc) within 5.0Å range: probe atom residue distance (Å) B Occ C:F403 b:54.3 occ:1.00 F01 C:JBF403 0.0 54.3 1.0 C02 C:JBF403 1.4 54.2 1.0 O D:HOH515 2.3 29.2 1.0 C07 C:JBF403 2.4 52.6 1.0 C03 C:JBF403 2.4 54.6 1.0 N09 C:JBF403 2.6 48.5 1.0 C08 C:JBF403 2.8 49.1 1.0 NH1 C:ARG134 2.9 11.9 1.0 CG C:ARG134 3.3 7.6 1.0 CD C:ARG134 3.3 9.3 1.0 ND1 D:HIS153 3.6 18.1 1.0 C04 C:JBF403 3.7 54.2 1.0 C06 C:JBF403 3.7 53.5 1.0 CZ C:ARG134 3.8 10.7 1.0 C10 C:JBF403 3.9 47.8 1.0 NE C:ARG134 4.0 10.2 1.0 CB D:HIS153 4.0 18.6 1.0 C05 C:JBF403 4.1 53.9 1.0 O21 C:JBF403 4.2 48.5 1.0 CG D:HIS153 4.2 18.5 1.0 CA D:HIS153 4.3 17.4 1.0 C12 C:JBF403 4.4 43.5 1.0 O C:ASP130 4.4 9.1 1.0 O7N D:NAP401 4.5 20.1 1.0 O C:HOH618 4.6 17.7 1.0 N20 C:JBF403 4.6 48.4 1.0 C11 C:JBF403 4.7 44.6 1.0 CE1 D:HIS153 4.7 18.6 1.0 CB C:ARG134 4.8 7.0 1.0 N D:HIS153 4.8 18.0 1.0 CB C:ASP130 5.0 9.9 1.0

M.Kim, J.H.Ha, J.Choi, B.R.Kim, V.Gapsys, K.O.Lee, J.G.Jee, K.S.Chakrabarti, B.L.De Groot, C.Griesinger, K.S.Ryu, D.Lee. Repositioning Food and Drug Administration-Approved Drugs For Inhibiting Biliverdin IX Beta Reductase B As A Novel Thrombocytopenia Therapeutic Target. J.Med.Chem. V. 65 2548 2022.
ISSN: ISSN 0022-2623
PubMed: 34957824
DOI: 10.1021/ACS.JMEDCHEM.1C01664