Fluorine in PDB 6xk9: Cereblon in Complex with DDB1, Cc-90009, and GSPT1

The structure of Cereblon in Complex with DDB1, Cc-90009, and GSPT1, PDB code: 6xk9 was solved by T.L.Clayton, E.T.Tran, J.Zhu, B.E.Pagarigan, M.E.Matyskiela, P.P.Chamberlain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.45 / 3.64
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.616, 112.041, 176.582, 90.00, 95.79, 90.00
R / Rfree (%)	20.8 / 24.6

The structure of Cereblon in Complex with DDB1, Cc-90009, and GSPT1 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Cereblon in Complex with DDB1, Cc-90009, and GSPT1 (pdb code 6xk9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cereblon in Complex with DDB1, Cc-90009, and GSPT1, PDB code: 6xk9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cereblon in Complex with DDB1, Cc-90009, and GSPT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cereblon in Complex with DDB1, Cc-90009, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ Z:F501 b:0.1 occ:1.00 F1 Z:V4M501 0.0 0.1 1.0 C16 Z:V4M501 1.4 91.0 1.0 F2 Z:V4M501 2.2 97.3 1.0 C15 Z:V4M501 2.3 80.9 1.0 C17 Z:V4M501 2.4 92.7 1.0 C18 Z:V4M501 2.7 92.0 1.0 N3 Z:V4M501 2.8 73.8 1.0 OE2 Z:GLU377 2.9 93.1 1.0 OE1 Z:GLU377 3.1 0.0 1.0 NZ X:LYS627 3.1 90.1 1.0 CD Z:GLU377 3.1 0.2 1.0 O4 Z:V4M501 3.4 78.9 1.0 OE1 X:GLN533 3.5 78.6 1.0 C22 Z:V4M501 3.6 91.1 1.0 CE X:LYS627 3.7 96.4 1.0 CD X:GLN533 4.0 84.7 1.0 C19 Z:V4M501 4.1 84.5 1.0 CG Z:GLU377 4.2 92.8 1.0 C14 Z:V4M501 4.2 71.0 1.0 NE2 X:GLN533 4.2 87.1 1.0 CD X:LYS627 4.3 97.3 1.0 C21 Z:V4M501 4.7 98.3 1.0 CG X:GLN533 4.9 72.4 1.0 C20 Z:V4M501 4.9 93.7 1.0

Fluorine binding site 2 out of 4 in the Cereblon in Complex with DDB1, Cc-90009, and GSPT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cereblon in Complex with DDB1, Cc-90009, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ Z:F501 b:97.3 occ:1.00 F2 Z:V4M501 0.0 97.3 1.0 C16 Z:V4M501 1.4 91.0 1.0 F1 Z:V4M501 2.2 0.1 1.0 C17 Z:V4M501 2.4 92.7 1.0 C15 Z:V4M501 2.4 80.9 1.0 C22 Z:V4M501 2.7 91.1 1.0 N3 Z:V4M501 3.1 73.8 1.0 CB Z:PRO352 3.1 68.5 1.0 O4 Z:V4M501 3.2 78.9 1.0 CG Z:PRO352 3.4 70.0 1.0 C18 Z:V4M501 3.6 92.0 1.0 C21 Z:V4M501 4.1 98.3 1.0 C14 Z:V4M501 4.4 71.0 1.0 OE2 Z:GLU377 4.5 93.1 1.0 NZ X:LYS627 4.5 90.1 1.0 CD Z:GLU377 4.5 0.2 1.0 CA Z:PRO352 4.6 63.7 1.0 C19 Z:V4M501 4.7 84.5 1.0 OE1 Z:GLU377 4.7 0.0 1.0 C3 Z:V4M501 4.8 65.4 1.0 CD Z:PRO352 4.9 64.3 1.0 C20 Z:V4M501 4.9 93.7 1.0 C2 Z:V4M501 4.9 63.1 1.0 CG Z:GLU377 4.9 92.8 1.0

Fluorine binding site 3 out of 4 in the Cereblon in Complex with DDB1, Cc-90009, and GSPT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cereblon in Complex with DDB1, Cc-90009, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:98.9 occ:1.00 F1 C:V4M501 0.0 98.9 1.0 C16 C:V4M501 1.4 96.3 1.0 F2 C:V4M501 2.2 0.5 1.0 C15 C:V4M501 2.4 83.5 1.0 C17 C:V4M501 2.4 98.9 1.0 C22 C:V4M501 2.7 97.0 1.0 N3 C:V4M501 3.1 75.2 1.0 O4 C:V4M501 3.2 79.3 1.0 CB C:PRO352 3.3 71.0 1.0 CG C:PRO352 3.3 70.8 1.0 C18 C:V4M501 3.7 93.2 1.0 C21 C:V4M501 4.0 96.3 1.0 NZ A:LYS627 4.3 92.8 1.0 C14 C:V4M501 4.4 66.1 1.0 C3 C:V4M501 4.7 60.2 1.0 C19 C:V4M501 4.8 86.2 1.0 OE2 C:GLU377 4.8 97.6 1.0 CA C:PRO352 4.8 66.8 1.0 CD C:PRO352 4.8 67.9 1.0 CE A:LYS627 4.9 89.9 1.0 C2 C:V4M501 4.9 57.8 1.0 C20 C:V4M501 4.9 94.1 1.0

Fluorine binding site 4 out of 4 in the Cereblon in Complex with DDB1, Cc-90009, and GSPT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cereblon in Complex with DDB1, Cc-90009, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:0.5 occ:1.00 F2 C:V4M501 0.0 0.5 1.0 C16 C:V4M501 1.4 96.3 1.0 F1 C:V4M501 2.2 98.9 1.0 C15 C:V4M501 2.4 83.5 1.0 C17 C:V4M501 2.4 98.9 1.0 N3 C:V4M501 2.8 75.2 1.0 NZ A:LYS627 2.9 92.8 1.0 C18 C:V4M501 3.0 93.2 1.0 OE2 C:GLU377 3.1 97.6 1.0 CE A:LYS627 3.2 89.9 1.0 C22 C:V4M501 3.4 97.0 1.0 O4 C:V4M501 3.4 79.3 1.0 OE1 A:GLN533 3.5 84.9 1.0 CD A:GLN533 4.0 84.9 1.0 C14 C:V4M501 4.2 66.1 1.0 CD A:LYS627 4.2 93.6 1.0 NE2 A:GLN533 4.2 88.9 1.0 C19 C:V4M501 4.3 86.2 1.0 CD C:GLU377 4.3 0.9 1.0 C21 C:V4M501 4.5 96.3 1.0 CB C:GLU377 4.8 82.6 1.0 C20 C:V4M501 4.9 94.1 1.0 CG A:GLN533 4.9 68.9 1.0

C.Surka, L.Jin, N.Mbong, C.C.Lu, I.S.Jang, E.Rychak, D.Mendy, T.Clayton, E.A.Tindall, C.Hsu, C.Fontanillo, E.Tran, A.Contreras, S.W.Ng, M.E.Matyskiela, K.Wang, P.P.Chamberlain, B.Cathers, J.Carmichael, J.D.Hansen, J.C.Y.Wang, M.D.Minden, J.Fan, D.W.Pierce, M.Pourdehnad, M.Rolfe, A.Lopez-Girona, J.E.Dick, G.Lu. Cc-90009, A Novel Cereblon E3 Ligase Modulator Targets Acute Myeloid Leukemia Blasts and Leukemia Stem Cells. Blood 2020.
ISSN: ESSN 1528-0020
PubMed: 33197925
DOI: 10.1182/BLOOD.2020008676