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

The structure of De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Mefuparib, PDB code: 8tnb 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)	78.12 / 1.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.206, 90.206, 202.113, 90, 90, 120
R / Rfree (%)	21.8 / 23.7

The binding sites of Fluorine atom in the De Novo Designed Protein Binds Poly Adp Ribose Polymerase Inhibitors (Parpi) - Holo Mefuparib (pdb code 8tnb). 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 Mefuparib, PDB code: 8tnb:
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 Mefuparib


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 Mefuparib within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:31.7 occ:1.00 F15 A:IQM201 0.0 31.7 1.0 C14 A:IQM201 1.4 29.8 1.0 C16 A:IQM201 2.4 26.6 1.0 C13 A:IQM201 2.4 27.5 1.0 HB2 A:PHE134 2.6 30.6 1.0 HD11 A:LEU90 2.8 29.0 1.0 HD2 A:PHE134 3.1 35.3 1.0 HD11 A:ILE21 3.1 31.0 1.0 HB1 A:ALA130 3.1 30.3 1.0 HD13 A:ILE21 3.3 31.0 1.0 CB A:PHE134 3.4 25.4 1.0 O A:ALA130 3.5 26.1 1.0 HA A:ASP131 3.5 37.6 1.0 CD2 A:PHE134 3.6 29.4 1.0 C17 A:IQM201 3.6 25.5 1.0 CD1 A:LEU90 3.6 24.1 1.0 C12 A:IQM201 3.6 26.2 1.0 CD1 A:ILE21 3.6 25.8 1.0 HD13 A:LEU90 3.7 29.0 1.0 HB3 A:PHE134 3.7 30.6 1.0 C A:ALA130 3.7 25.0 1.0 CG A:PHE134 3.8 28.8 1.0 HB3 A:ALA130 3.8 30.3 1.0 CB A:ALA130 3.9 25.2 1.0 HG12 A:ILE21 4.0 28.3 1.0 HD12 A:LEU90 4.0 29.0 1.0 C21 A:IQM201 4.1 24.9 1.0 N A:ASP131 4.1 25.5 1.0 HG22 A:VAL94 4.2 27.9 1.0 HD21 A:LEU90 4.2 29.4 1.0 H A:PHE134 4.2 31.0 1.0 CA A:ASP131 4.3 31.3 1.0 HG21 A:VAL94 4.3 27.9 1.0 CA A:ALA130 4.4 26.0 1.0 HD12 A:ILE21 4.4 31.0 1.0 CG1 A:ILE21 4.4 23.5 1.0 HG11 A:VAL57 4.5 29.9 1.0 HG23 A:VAL94 4.5 27.9 1.0 CG2 A:VAL94 4.5 23.2 1.0 CE2 A:PHE134 4.6 32.9 1.0 CA A:PHE134 4.6 27.3 1.0 H A:ASP131 4.6 30.6 1.0 HB2 A:ALA130 4.7 30.3 1.0 HG21 A:ILE21 4.7 28.5 1.0 HA A:ALA130 4.7 31.2 1.0 HG13 A:VAL57 4.8 29.9 1.0 N A:PHE134 4.8 25.8 1.0 HA A:PHE134 4.8 32.8 1.0 CG A:LEU90 4.8 21.9 1.0 HE2 A:PHE134 4.8 39.6 1.0 C18 A:IQM201 4.8 28.1 1.0 CD1 A:PHE134 4.9 37.9 1.0 CD2 A:LEU90 4.9 24.4 1.0 C11 A:IQM201 5.0 28.0 1.0 O20 A:IQM201 5.0 29.4 1.0

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


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 Mefuparib within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:30.1 occ:1.00 F15 B:IQM201 0.0 30.1 1.0 C14 B:IQM201 1.4 30.4 1.0 C13 B:IQM201 2.4 29.5 1.0 C16 B:IQM201 2.4 28.0 1.0 HB2 B:PHE134 2.7 34.9 1.0 HD11 B:LEU90 2.8 32.2 1.0 HD11 B:ILE21 3.0 29.1 1.0 HD2 B:PHE134 3.0 34.3 1.0 HD13 B:ILE21 3.0 29.1 1.0 HB1 B:ALA130 3.2 32.7 1.0 CD1 B:ILE21 3.4 24.2 1.0 CD2 B:PHE134 3.5 28.5 1.0 CB B:PHE134 3.6 29.1 1.0 HA B:ASP131 3.6 35.9 1.0 O B:ALA130 3.6 27.6 1.0 C17 B:IQM201 3.6 26.4 1.0 C12 B:IQM201 3.6 27.7 1.0 CD1 B:LEU90 3.7 26.8 1.0 HB3 B:ALA130 3.7 32.7 1.0 CG B:PHE134 3.8 25.8 1.0 HG12 B:ILE21 3.8 26.3 1.0 C B:ALA130 3.8 26.2 1.0 HD13 B:LEU90 3.8 32.2 1.0 CB B:ALA130 3.9 27.2 1.0 HB3 B:PHE134 3.9 34.9 1.0 HD12 B:LEU90 4.0 32.2 1.0 N B:ASP131 4.1 27.1 1.0 C21 B:IQM201 4.1 24.6 1.0 HG22 B:VAL94 4.2 29.3 1.0 CG1 B:ILE21 4.2 21.9 1.0 HD12 B:ILE21 4.2 29.1 1.0 HD21 B:LEU90 4.2 31.9 1.0 CA B:ASP131 4.3 29.9 1.0 CE2 B:PHE134 4.4 26.6 1.0 HG11 B:VAL57 4.4 28.8 1.0 HG21 B:VAL94 4.4 29.3 1.0 CA B:ALA130 4.5 26.1 1.0 HG21 B:ILE21 4.5 29.4 1.0 H B:PHE134 4.5 32.2 1.0 H B:ASP131 4.5 32.5 1.0 HG23 B:VAL94 4.6 29.3 1.0 CG2 B:VAL94 4.6 24.3 1.0 HE2 B:PHE134 4.6 32.0 1.0 OD1 B:ASP131 4.6 46.8 1.0 HB2 B:ALA130 4.7 32.7 1.0 HG13 B:VAL57 4.7 28.8 1.0 HG13 B:ILE21 4.8 26.3 1.0 CA B:PHE134 4.8 26.4 1.0 CG B:LEU90 4.8 25.3 1.0 CD1 B:PHE134 4.9 34.5 1.0 HA B:ALA130 4.9 31.4 1.0 CD2 B:LEU90 4.9 26.6 1.0 C18 B:IQM201 4.9 28.7 1.0 HA B:PHE134 4.9 31.8 1.0 HD22 B:LEU90 5.0 31.9 1.0 HZ3 B:TRP18 5.0 61.5 1.0 CG1 B:VAL57 5.0 23.9 1.0 N B:PHE134 5.0 26.8 1.0 C11 B:IQM201 5.0 28.4 1.0

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


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 Mefuparib within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:33.0 occ:1.00 F15 C:IQM201 0.0 33.0 1.0 C14 C:IQM201 1.4 29.3 1.0 C16 C:IQM201 2.3 25.3 1.0 C13 C:IQM201 2.4 31.8 1.0 HB2 C:PHE134 2.5 39.7 1.0 HD11 C:LEU90 2.9 35.1 1.0 HD11 C:ILE21 2.9 30.4 1.0 HD13 C:ILE21 2.9 30.4 1.0 CB C:PHE134 3.3 33.0 1.0 CD1 C:ILE21 3.4 25.3 1.0 HB1 C:ALA130 3.4 34.1 1.0 HA C:ASP131 3.5 40.9 1.0 O C:ALA130 3.6 30.7 1.0 HD1 C:PHE134 3.6 37.0 1.0 HB3 C:PHE134 3.6 39.7 1.0 C17 C:IQM201 3.6 27.4 1.0 C12 C:IQM201 3.6 33.8 1.0 CG C:PHE134 3.6 31.4 1.0 HG12 C:ILE21 3.7 29.6 1.0 CD1 C:LEU90 3.7 29.2 1.0 CD1 C:PHE134 3.8 30.8 1.0 HD13 C:LEU90 3.8 35.1 1.0 C C:ALA130 3.8 30.8 1.0 HD21 C:LEU90 3.9 37.1 1.0 HB3 C:ALA130 4.0 34.1 1.0 CB C:ALA130 4.1 28.3 1.0 C21 C:IQM201 4.1 26.1 1.0 CG1 C:ILE21 4.1 24.6 1.0 N C:ASP131 4.2 33.9 1.0 HD12 C:ILE21 4.2 30.4 1.0 H C:PHE134 4.2 37.5 1.0 HG11 C:VAL57 4.2 31.3 1.0 CA C:ASP131 4.3 34.1 1.0 HD12 C:LEU90 4.3 35.1 1.0 HG11 C:VAL94 4.4 30.6 1.0 HG21 C:ILE21 4.4 29.9 1.0 HG12 C:VAL94 4.5 30.6 1.0 HG13 C:VAL57 4.5 31.3 1.0 CA C:PHE134 4.5 30.0 1.0 CD2 C:PHE134 4.5 34.4 1.0 CA C:ALA130 4.6 31.0 1.0 CD2 C:LEU90 4.6 30.9 1.0 H C:ASP131 4.6 40.7 1.0 HD22 C:LEU90 4.7 37.1 1.0 HG13 C:ILE21 4.7 29.6 1.0 HA C:PHE134 4.7 36.1 1.0 CE1 C:PHE134 4.7 28.0 1.0 N C:PHE134 4.7 31.2 1.0 CG C:LEU90 4.8 26.2 1.0 OD1 C:ASP131 4.8 49.2 1.0 CG1 C:VAL94 4.8 25.4 1.0 CG1 C:VAL57 4.8 26.0 1.0 C18 C:IQM201 4.8 27.4 1.0 HD2 C:PHE134 4.9 41.4 1.0 HA C:ALA130 4.9 37.2 1.0 HG13 C:VAL94 4.9 30.6 1.0 HB2 C:ALA130 4.9 34.1 1.0 O20 C:IQM201 5.0 29.2 1.0 C11 C:IQM201 5.0 32.4 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