Fluorine in PDB 5n2f: Structure of Pd-L1/Small-Molecule Inhibitor Complex

The structure of Structure of Pd-L1/Small-Molecule Inhibitor Complex, PDB code: 5n2f was solved by K.Guzik, K.M.Zak, P.Grudnik, G.Dubin, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.84 / 1.70
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.815, 52.379, 111.526, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23

The binding sites of Fluorine atom in the Structure of Pd-L1/Small-Molecule Inhibitor Complex (pdb code 5n2f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Pd-L1/Small-Molecule Inhibitor Complex, PDB code: 5n2f:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Pd-L1/Small-Molecule Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Pd-L1/Small-Molecule Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:59.8 occ:1.00 F1 B:8HW201 0.0 59.8 1.0 C19 B:8HW201 1.4 57.6 1.0 C2 B:8HW201 2.4 42.9 1.0 C20 B:8HW201 2.4 56.6 1.0 O B:8HW201 2.7 25.8 1.0 CG2 B:ILE54 3.4 26.5 1.0 CG2 B:VAL68 3.5 39.5 1.0 C1 B:8HW201 3.6 44.1 1.0 C21 B:8HW201 3.6 56.2 1.0 CB B:TYR56 3.9 23.2 1.0 CD1 B:TYR56 4.1 30.6 1.0 C3 B:8HW201 4.1 28.4 1.0 C B:8HW201 4.1 49.1 1.0 CG B:TYR56 4.3 25.1 1.0 CB B:GLN66 4.3 29.8 1.0 O A:ALA121 4.3 25.7 1.0 CD B:GLN66 4.4 39.8 1.0 C18 B:8HW201 4.4 25.5 1.0 NE2 B:GLN66 4.4 39.7 1.0 OE1 B:GLN66 4.5 45.6 1.0 O A:HOH250 4.7 40.7 1.0 C4 B:8HW201 4.7 24.4 1.0 O B:VAL55 4.8 30.1 1.0 CG B:GLN66 4.9 36.2 1.0 CB B:VAL68 4.9 38.7 1.0 CA B:TYR56 4.9 21.2 1.0 C22 B:8HW201 4.9 56.2 1.0 CB B:ILE54 4.9 32.4 1.0 O A:HOH264 5.0 38.2 1.0

Fluorine binding site 2 out of 2 in the Structure of Pd-L1/Small-Molecule Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Pd-L1/Small-Molecule Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:43.6 occ:1.00 F B:8HW201 0.0 43.6 1.0 C B:8HW201 1.4 49.1 1.0 C21 B:8HW201 2.4 56.2 1.0 C1 B:8HW201 2.4 44.1 1.0 C22 B:8HW201 2.8 56.2 1.0 O A:HOH229 3.0 39.5 1.0 N B:8HW201 3.1 57.0 1.0 O B:HOH394 3.2 57.2 1.0 OD1 A:ASP122 3.4 27.0 1.0 C2 B:8HW201 3.6 42.9 1.0 C20 B:8HW201 3.6 56.6 1.0 CE1 B:TYR56 3.7 32.5 1.0 CZ B:TYR56 3.8 21.8 1.0 CE2 A:TYR123 3.8 39.1 1.0 OH B:TYR56 3.8 26.2 1.0 O A:HOH269 3.8 55.7 1.0 C23 B:8HW201 4.0 61.7 1.0 CD2 A:TYR123 4.0 26.3 1.0 OD1 B:ASN63 4.0 43.7 1.0 C19 B:8HW201 4.1 57.6 1.0 CD1 B:TYR56 4.5 30.6 1.0 CE2 B:TYR56 4.5 25.5 1.0 CG A:ASP122 4.6 36.8 1.0 CZ A:TYR123 4.7 46.1 1.0 O B:8HW201 4.8 25.8 1.0 CG B:ASN63 4.9 45.8 1.0 O A:TYR123 4.9 26.1 1.0 O B:HOH405 4.9 60.5 1.0 C3 B:8HW201 4.9 28.4 1.0 N A:TYR123 4.9 23.3 1.0

K.Guzik, K.M.Zak, P.Grudnik, K.Magiera, B.Musielak, R.Torner, L.Skalniak, A.Domling, G.Dubin, T.A.Holak. Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (Pd-1/Pd-L1) Interaction Via Transiently Induced Protein States and Dimerization of Pd-L1. J. Med. Chem. V. 60 5857 2017.
ISSN: ISSN 1520-4804
PubMed: 28613862
DOI: 10.1021/ACS.JMEDCHEM.7B00293