Fluorine in PDB 9ery: Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor

The structure of Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor, PDB code: 9ery was solved by J.Plewka, K.Magiera-Mularz, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.36 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.534, 74.534, 95.392, 90, 90, 120
R / Rfree (%)	22.2 / 27.6

The binding sites of Fluorine atom in the Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor (pdb code 9ery). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor, PDB code: 9ery:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:170.0 occ:1.00 F1 A:VVH201 0.0 170.0 1.0 C13 A:VVH201 1.4 131.6 1.0 H7 A:VVH201 1.9 143.0 1.0 F2 A:VVH201 2.2 191.9 1.0 C12 A:VVH201 2.4 105.1 1.0 H3 A:VVH201 2.6 100.9 1.0 O A:ASP108 2.8 89.0 1.0 H9 A:VVH201 3.1 105.8 1.0 HB1 A:ALA107 3.1 94.7 1.0 HB3 A:MET101 3.1 91.2 1.0 C7 A:VVH201 3.2 101.9 1.0 C6 A:VVH201 3.2 99.2 1.0 H A:ASP108 3.2 97.6 1.0 C A:ASP108 3.2 96.2 1.0 HB3 A:TYR109 3.3 94.1 1.0 C11 A:VVH201 3.3 100.1 1.0 N A:ASP108 3.5 96.0 1.0 C5 A:VVH201 3.5 100.7 1.0 HA A:MET101 3.5 89.1 1.0 H A:ILE102 3.7 95.9 1.0 C14 A:VVH201 3.7 108.2 1.0 O A:ILE102 3.7 108.8 1.0 CA A:ASP108 3.8 107.5 1.0 HA A:ASP108 3.8 100.8 1.0 CB A:MET101 3.9 88.0 1.0 N A:TYR109 3.9 80.7 1.0 CB A:ALA107 4.0 94.7 1.0 HD2 A:TYR109 4.0 97.2 1.0 CA A:MET101 4.0 88.4 1.0 N A:ILE102 4.1 95.1 1.0 HG2 A:MET101 4.1 100.8 1.0 C A:ALA107 4.1 92.4 1.0 CB A:TYR109 4.2 97.8 1.0 C1 A:VVH201 4.2 103.7 1.0 HA A:ALA107 4.3 97.3 1.0 H8 A:VVH201 4.3 105.4 1.0 C A:MET101 4.3 96.0 1.0 H A:TYR109 4.4 85.7 1.0 CA A:ALA107 4.4 94.6 1.0 C A:ILE102 4.4 92.4 1.0 CG A:MET101 4.4 99.4 1.0 C8 A:VVH201 4.5 100.7 1.0 HB3 A:ALA107 4.5 94.7 1.0 CA A:TYR109 4.5 86.1 1.0 HA A:TYR109 4.5 85.8 1.0 H1 A:VVH201 4.5 104.9 1.0 C10 A:VVH201 4.5 97.7 1.0 HB2 A:ALA107 4.6 94.7 1.0 HB2 A:MET101 4.6 90.8 1.0 HB2 A:TYR109 4.7 94.2 1.0 O1 A:VVH201 4.7 104.4 1.0 C4 A:VVH201 4.7 119.4 1.0 CD2 A:TYR109 4.8 95.2 1.0 SD A:MET101 4.8 123.8 1.0 CA A:ILE102 4.9 98.3 1.0 HB2 A:SER103 4.9 101.2 1.0 O A:ALA107 5.0 95.2 1.0

Fluorine binding site 2 out of 2 in the Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Strucutre of Pd-L1 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:191.9 occ:1.00 F2 A:VVH201 0.0 191.9 1.0 C13 A:VVH201 1.4 131.6 1.0 H7 A:VVH201 1.8 143.0 1.0 F1 A:VVH201 2.2 170.0 1.0 C12 A:VVH201 2.4 105.1 1.0 HB3 A:MET101 2.6 91.2 1.0 C5 A:VVH201 2.9 100.7 1.0 C7 A:VVH201 2.9 101.9 1.0 SD A:MET101 3.0 123.8 1.0 HG2 A:MET101 3.2 100.8 1.0 C6 A:VVH201 3.2 99.2 1.0 SD B:MET101 3.2 122.6 1.0 H3 A:VVH201 3.3 100.9 1.0 HB3 A:TYR109 3.3 94.1 1.0 CG A:MET101 3.3 99.4 1.0 CB A:MET101 3.3 88.0 1.0 HE1 A:MET101 3.4 137.0 1.0 C4 A:VVH201 3.6 119.4 1.0 C11 A:VVH201 3.6 100.1 1.0 HD2 A:TYR109 3.7 97.2 1.0 CE A:MET101 3.7 142.2 1.0 H9 A:VVH201 3.8 105.8 1.0 H2 A:VVH201 3.9 114.8 1.0 HA A:MET101 3.9 89.1 1.0 HE3 A:MET101 4.0 137.3 1.0 HB2 A:MET101 4.0 90.8 1.0 HB3 B:MET101 4.0 95.5 1.0 C1 A:VVH201 4.0 103.7 1.0 C14 A:VVH201 4.2 108.2 1.0 CA A:MET101 4.2 88.4 1.0 CB A:TYR109 4.2 97.8 1.0 C8 A:VVH201 4.3 100.7 1.0 HG3 A:MET101 4.3 100.6 1.0 C3 A:VVH201 4.3 121.1 1.0 CD2 A:TYR109 4.4 95.2 1.0 H8 A:VVH201 4.4 105.4 1.0 HE3 B:MET101 4.4 110.3 1.0 CE B:MET101 4.4 106.5 1.0 C2 A:VVH201 4.5 113.2 1.0 HB2 A:TYR109 4.5 94.2 1.0 HE2 A:MET101 4.5 137.3 1.0 O A:ASP108 4.6 89.0 1.0 H1 A:VVH201 4.6 104.9 1.0 CG B:MET101 4.6 101.9 1.0 HE2 B:MET101 4.7 110.3 1.0 CB B:MET101 4.7 93.7 1.0 HB1 A:ALA107 4.7 94.7 1.0 C10 A:VVH201 4.7 97.7 1.0 CG A:TYR109 4.7 93.9 1.0 HB2 B:MET101 4.8 95.4 1.0 H4 A:VVH201 4.8 99.5 1.0 C A:ASP108 4.9 96.2 1.0 C A:MET101 5.0 96.0 1.0

F.Zhang, H.Zhang, S.Zhou, J.Plewka, M.Wang, S.Sun, C.Wu, Q.Yu, M.Zhu, A.Awadasseid, Y.Wu, K.Magiera-Mularz, W.Zhang. Design, Synthesis, and Evaluation of Antitumor Activity of 2-Arylmethoxy-4-(2-Fluoromethyl-Biphenyl-3-Ylmethoxy) Benzylamine Derivatives As Pd-1/Pd-L1 Inhibitors Eur.J.Med.Chem. 2024.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2024.116683