Fluorine in PDB 6xib: PCSK9(Deltacrd) in Complex with Cyclic Peptide 30

The structure of PCSK9(Deltacrd) in Complex with Cyclic Peptide 30, PDB code: 6xib was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.51 / 1.55
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.027, 71.027, 152.357, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 20.5

The binding sites of Fluorine atom in the PCSK9(Deltacrd) in Complex with Cyclic Peptide 30 (pdb code 6xib). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the PCSK9(Deltacrd) in Complex with Cyclic Peptide 30, PDB code: 6xib:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the PCSK9(Deltacrd) in Complex with Cyclic Peptide 30


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PCSK9(Deltacrd) in Complex with Cyclic Peptide 30 within 5.0Å range: probe atom residue distance (Å) B Occ I:F5 b:26.1 occ:1.00 F I:FTR5 0.0 26.1 1.0 CZ3 I:FTR5 1.4 24.3 1.0 CE3 I:FTR5 2.3 22.8 1.0 CH2 I:FTR5 2.4 23.8 1.0 CD2 I:FTR5 3.6 21.4 1.0 CZ2 I:FTR5 3.6 23.0 1.0 N I:ASP7 3.7 20.0 1.0 CB I:ASP7 3.9 23.1 1.0 C I:FTR6 4.1 20.3 1.0 O I:HOH110 4.1 27.9 1.0 CE2 I:FTR5 4.1 22.0 1.0 O I:HOH105 4.1 29.4 1.0 CA I:ASP7 4.3 20.3 1.0 CA I:FTR6 4.3 20.2 1.0 CG I:ASP7 4.5 28.1 1.0 O I:FTR5 4.7 19.9 1.0 N I:FTR6 4.7 19.7 1.0 O I:FTR6 4.8 20.2 1.0 C I:FTR5 4.9 19.9 1.0 O I:HOH114 4.9 39.0 1.0 CG I:FTR5 5.0 20.7 1.0 OD1 I:ASP7 5.0 28.6 1.0 OD2 I:ASP7 5.0 30.2 1.0

Fluorine binding site 2 out of 2 in the PCSK9(Deltacrd) in Complex with Cyclic Peptide 30


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PCSK9(Deltacrd) in Complex with Cyclic Peptide 30 within 5.0Å range: probe atom residue distance (Å) B Occ I:F6 b:20.1 occ:1.00 F I:FTR6 0.0 20.1 1.0 CZ3 I:FTR6 1.4 20.6 1.0 CE3 I:FTR6 2.3 20.2 1.0 CH2 I:FTR6 2.4 21.3 1.0 C B:VAL380 3.1 17.3 1.0 N B:SER381 3.1 16.6 1.0 CA B:VAL380 3.3 16.7 1.0 O I:GLY4 3.4 20.7 1.0 N B:VAL380 3.5 16.5 1.0 CG1 B:ILE369 3.5 19.2 1.0 O B:VAL380 3.6 17.9 1.0 CD2 I:FTR6 3.6 20.8 1.0 CZ2 I:FTR6 3.6 21.9 1.0 C B:PHE379 3.8 17.6 1.0 CA B:SER381 3.8 17.4 1.0 C I:GLY4 3.9 21.2 1.0 O B:PHE379 3.9 18.2 1.0 CG2 B:ILE369 4.0 18.7 1.0 CB B:SER381 4.0 18.3 1.0 CB B:ILE369 4.0 18.4 1.0 CA B:ILE369 4.1 17.7 1.0 CE2 I:FTR6 4.1 21.8 1.0 O I:CYS2 4.4 24.7 1.0 CB B:PHE379 4.4 17.5 1.0 N I:FTR5 4.5 19.9 1.0 CD1 B:ILE369 4.6 20.5 1.0 OG B:SER381 4.6 19.5 1.0 CA I:FTR5 4.6 20.1 1.0 CA I:GLY4 4.6 21.9 1.0 N I:GLY4 4.7 22.2 1.0 CA B:PHE379 4.7 17.3 1.0 CB B:VAL380 4.8 17.2 1.0 CG I:3WX10 4.8 23.9 1.0 N B:GLY370 4.8 17.2 1.0 CG I:FTR6 4.9 21.0 1.0 C B:ILE369 5.0 17.8 1.0

C.Alleyne, R.P.Amin, B.Bhatt, E.Bianchi, J.C.Blain, N.Boyer, D.Branca, M.W.Embrey, S.N.Ha, K.Jette, D.G.Johns, A.D.Kerekes, K.A.Koeplinger, D.Laplaca, N.Li, B.Murphy, P.Orth, A.Ricardo, S.Salowe, K.Seyb, A.Shahripour, J.R.Stringer, Y.Sun, R.Tracy, C.Wu, Y.Xiong, H.Youm, H.J.Zokian, T.J.Tucker. Series of Novel and Highly Potent Cyclic Peptide PCSK9 Inhibitors Derived From An Mrna Display Screen and Optimized Via Structure-Based Design. J.Med.Chem. V. 63 13796 2020.
ISSN: ISSN 0022-2623
PubMed: 33170686
DOI: 10.1021/ACS.JMEDCHEM.0C01084