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

Protein crystallography data

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

Other elements in 6xk9:

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

Fluorine Binding Sites:

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 6xk9

Go back to Fluorine Binding Sites List in 6xk9
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 6xk9

Go back to Fluorine Binding Sites List in 6xk9
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 6xk9

Go back to Fluorine Binding Sites List in 6xk9
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 6xk9

Go back to Fluorine Binding Sites List in 6xk9
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

Reference:

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
Page generated: Sun Dec 13 13:36:43 2020

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