Fluorine in PDB 8tn6: De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib

The structure of De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib, PDB code: 8tn6 was solved by L.Lu, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 1.36
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.252, 91.252, 201.951, 90, 90, 120
R / Rfree (%)	19.5 / 21.7

The binding sites of Fluorine atom in the De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib (pdb code 8tn6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib, PDB code: 8tn6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:22.6 occ:1.00 F1 A:RPB201 0.0 22.6 1.0 C2 A:RPB201 1.4 21.3 1.0 C1 A:RPB201 2.3 20.5 1.0 C3 A:RPB201 2.4 21.4 1.0 H3 A:RPB201 2.5 25.7 1.0 HA A:RPB201 2.5 24.6 1.0 HD13 A:ILE21 2.6 24.7 1.0 HB1 A:ALA130 2.8 23.4 1.0 HD11 A:ILE21 2.8 24.7 1.0 CD1 A:ILE21 3.2 20.6 1.0 HD11 A:LEU90 3.2 21.9 1.0 HB2 A:PHE134 3.2 25.6 1.0 HB3 A:ALA130 3.4 23.4 1.0 HD2 A:PHE134 3.4 28.0 1.0 CB A:ALA130 3.5 19.5 1.0 C6 A:RPB201 3.5 20.4 1.0 HG12 A:ILE21 3.5 21.4 1.0 HA A:ASP131 3.7 27.6 1.0 C A:ALA130 3.7 19.9 1.0 O A:ALA130 3.7 21.0 1.0 C4 A:RPB201 3.7 19.7 1.0 HG21 A:ILE21 3.8 21.1 1.0 CG1 A:ILE21 3.9 17.8 1.0 HD12 A:ILE21 3.9 24.7 1.0 CD2 A:PHE134 4.0 23.3 1.0 N A:ASP131 4.0 20.7 1.0 C5 A:RPB201 4.0 20.7 1.0 CB A:PHE134 4.0 21.3 1.0 CD1 A:LEU90 4.1 18.2 1.0 HG12 A:VAL94 4.2 23.2 1.0 CA A:ALA130 4.2 20.4 1.0 HB3 A:PHE134 4.2 25.6 1.0 HB2 A:ALA130 4.3 23.4 1.0 HG11 A:VAL94 4.3 23.2 1.0 HD12 A:LEU90 4.3 21.9 1.0 HD13 A:LEU90 4.3 21.9 1.0 HZ3 A:TRP18 4.3 45.3 1.0 CA A:ASP131 4.3 23.0 1.0 CG A:PHE134 4.3 23.2 1.0 H A:ASP131 4.4 24.9 1.0 HG11 A:VAL57 4.5 21.3 1.0 HG13 A:ILE21 4.6 21.4 1.0 CG1 A:VAL94 4.6 19.3 1.0 CG2 A:ILE21 4.6 17.6 1.0 HA A:ALA130 4.7 24.6 1.0 C7 A:RPB201 4.7 20.5 1.0 HG23 A:ILE21 4.8 21.1 1.0 N2 A:RPB201 4.8 21.1 1.0 HB2 A:ASP131 4.8 32.7 1.0 H A:PHE134 4.8 23.6 1.0 O1 A:RPB201 4.8 21.2 1.0 HD21 A:LEU90 4.8 24.4 1.0 CE2 A:PHE134 4.9 22.4 1.0 HG13 A:VAL94 4.9 23.2 1.0 CB A:ILE21 4.9 16.7 1.0 HG13 A:VAL57 5.0 21.3 1.0 HE2 A:PHE134 5.0 26.9 1.0

Fluorine binding site 2 out of 3 in the De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:22.1 occ:1.00 F1 B:RPB201 0.0 22.1 1.0 C2 B:RPB201 1.4 20.7 1.0 C1 B:RPB201 2.3 22.7 1.0 C3 B:RPB201 2.3 22.2 1.0 H3 B:RPB201 2.5 26.6 1.0 HA B:RPB201 2.5 27.2 1.0 HD13 B:ILE21 2.7 26.1 1.0 HD11 B:ILE21 2.8 26.1 1.0 HB1 B:ALA130 3.0 21.4 1.0 HB2 B:PHE134 3.1 25.5 1.0 CD1 B:ILE21 3.2 21.7 1.0 HD11 B:LEU90 3.2 22.7 1.0 C6 B:RPB201 3.5 20.3 1.0 HG12 B:ILE21 3.5 24.9 1.0 HB3 B:ALA130 3.6 21.4 1.0 HA B:ASP131 3.6 26.8 1.0 CB B:ALA130 3.7 17.8 1.0 HD1 B:PHE134 3.7 30.0 1.0 O B:ALA130 3.7 19.2 1.0 C4 B:RPB201 3.7 19.2 1.0 C B:ALA130 3.8 17.8 1.0 CB B:PHE134 3.9 21.2 1.0 CG1 B:ILE21 3.9 20.7 1.0 HD12 B:ILE21 4.0 26.1 1.0 HG21 B:ILE21 4.0 24.9 1.0 C5 B:RPB201 4.0 22.3 1.0 CD1 B:LEU90 4.0 18.9 1.0 CD1 B:PHE134 4.0 25.0 1.0 N B:ASP131 4.1 18.9 1.0 HB3 B:PHE134 4.1 25.5 1.0 HD13 B:LEU90 4.2 22.7 1.0 CG B:PHE134 4.2 21.8 1.0 HG12 B:VAL94 4.2 23.1 1.0 HG11 B:VAL94 4.2 23.1 1.0 HD12 B:LEU90 4.3 22.7 1.0 CA B:ASP131 4.3 22.3 1.0 CA B:ALA130 4.3 18.4 1.0 HG11 B:VAL57 4.3 23.1 1.0 HB2 B:ALA130 4.5 21.4 1.0 H B:ASP131 4.5 22.7 1.0 HG13 B:ILE21 4.6 24.9 1.0 CG1 B:VAL94 4.6 19.2 1.0 C7 B:RPB201 4.6 20.3 1.0 H B:PHE134 4.7 22.7 1.0 HA B:ALA130 4.7 22.1 1.0 CG2 B:ILE21 4.7 20.7 1.0 HD21 B:LEU90 4.7 24.7 1.0 N2 B:RPB201 4.8 20.0 1.0 O1 B:RPB201 4.8 21.9 1.0 HG13 B:VAL94 4.8 23.1 1.0 HG23 B:ILE21 4.8 24.9 1.0 HB2 B:ASP131 4.9 32.5 1.0 HG13 B:VAL57 4.9 23.1 1.0 CB B:ILE21 4.9 17.7 1.0 CE1 B:PHE134 5.0 24.0 1.0

Fluorine binding site 3 out of 3 in the De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:22.0 occ:1.00 F1 C:RPB201 0.0 22.0 1.0 C2 C:RPB201 1.4 21.2 1.0 C1 C:RPB201 2.3 21.0 1.0 C3 C:RPB201 2.3 20.1 1.0 H3 C:RPB201 2.5 24.2 1.0 HA C:RPB201 2.5 25.2 1.0 HD13 C:ILE21 2.6 26.4 1.0 HB2 C:PHE134 2.7 27.6 1.0 HD11 C:ILE21 2.8 26.4 1.0 HD11 C:LEU90 3.0 24.9 1.0 HB1 C:ALA130 3.1 24.0 1.0 CD1 C:ILE21 3.1 22.0 1.0 HG12 C:ILE21 3.5 21.9 1.0 C6 C:RPB201 3.5 21.2 1.0 CB C:PHE134 3.5 23.0 1.0 O C:ALA130 3.6 21.3 1.0 HD1 C:PHE134 3.7 30.9 1.0 C4 C:RPB201 3.7 18.6 1.0 HB3 C:PHE134 3.7 27.6 1.0 HA C:ASP131 3.8 28.1 1.0 C C:ALA130 3.8 21.3 1.0 HG21 C:ILE21 3.8 24.9 1.0 HB3 C:ALA130 3.9 24.0 1.0 CB C:ALA130 3.9 19.9 1.0 CD1 C:LEU90 3.9 20.7 1.0 CG1 C:ILE21 3.9 18.2 1.0 CG C:PHE134 3.9 20.6 1.0 HD12 C:ILE21 3.9 26.4 1.0 CD1 C:PHE134 3.9 25.7 1.0 C5 C:RPB201 4.0 22.2 1.0 HD13 C:LEU90 4.1 24.9 1.0 HD21 C:LEU90 4.2 26.0 1.0 N C:ASP131 4.2 22.5 1.0 HD12 C:LEU90 4.3 24.9 1.0 HG11 C:VAL57 4.3 22.8 1.0 HG11 C:VAL94 4.4 24.2 1.0 HG12 C:VAL94 4.4 24.2 1.0 H C:PHE134 4.4 27.4 1.0 CA C:ALA130 4.5 20.4 1.0 CA C:ASP131 4.5 23.4 1.0 HG13 C:ILE21 4.5 21.9 1.0 HB2 C:ALA130 4.6 24.0 1.0 CG2 C:ILE21 4.6 20.8 1.0 C7 C:RPB201 4.7 20.7 1.0 H C:ASP131 4.7 27.1 1.0 HA C:ALA130 4.8 24.6 1.0 HG23 C:ILE21 4.8 24.9 1.0 CD2 C:PHE134 4.8 24.2 1.0 CG1 C:VAL94 4.8 20.1 1.0 CA C:PHE134 4.8 21.5 1.0 N2 C:RPB201 4.8 21.9 1.0 HG13 C:VAL57 4.8 22.8 1.0 O1 C:RPB201 4.8 20.7 1.0 CE1 C:PHE134 4.9 25.1 1.0 HZ3 C:TRP18 4.9 38.8 1.0 CD2 C:LEU90 4.9 21.6 1.0 CB C:ILE21 4.9 17.7 1.0 CG C:LEU90 4.9 19.0 1.0 HG13 C:VAL94 4.9 24.2 1.0 N C:PHE134 5.0 22.8 1.0 CG1 C:VAL57 5.0 18.9 1.0 HD22 C:LEU90 5.0 26.0 1.0

L.Lu, X.Gou, S.K.Tan, S.I.Mann, H.Yang, X.Zhong, D.Gazgalis, J.Valdiviezo, H.Jo, Y.Wu, M.E.Diolaiti, A.Ashworth, N.F.Polizzi, W.F.Degrado. De Novo Design of Drug-Binding Proteins with Predictable Binding Energy and Specificity. Science V. 384 106 2024.
ISSN: ESSN 1095-9203
PubMed: 38574125
DOI: 10.1126/SCIENCE.ADL5364