Fluorine in PDB 7jto: Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb

The structure of Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb, PDB code: 7jto was solved by J.Kottur, R.Jain, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.96 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.38, 187.83, 49.15, 90, 116.96, 90
R / Rfree (%)	20 / 22.5

The structure of Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb (pdb code 7jto). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb, PDB code: 7jto:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ B:F406 b:19.6 occ:1.00 F82 B:VKA406 0.0 19.6 1.0 C80 B:VKA406 1.4 21.9 1.0 F84 B:VKA406 2.2 21.7 1.0 F83 B:VKA406 2.2 24.6 1.0 C79 B:VKA406 2.4 20.1 1.0 C78 B:VKA406 2.8 21.5 1.0 CB B:SER49 3.4 17.2 1.0 CA B:SER49 3.6 18.4 1.0 CD2 B:LEU321 3.6 19.6 1.0 C74 B:VKA406 3.7 19.1 1.0 CB B:ALA47 3.8 20.7 1.0 N B:SER49 4.0 18.1 1.0 O B:HOH513 4.0 38.3 1.0 O B:VAL48 4.1 20.5 1.0 C B:VAL48 4.2 16.6 1.0 C77 B:VKA406 4.2 23.1 1.0 C73 B:VKA406 4.4 16.1 1.0 C B:ALA47 4.5 19.7 1.0 O85 B:VKA406 4.5 21.8 1.0 O B:ALA47 4.5 19.5 1.0 OG B:SER49 4.6 17.1 1.0 C75 B:VKA406 4.8 21.2 1.0 CA B:ALA47 4.8 22.8 1.0 N B:VAL48 4.8 18.8 1.0 C B:SER49 4.9 16.1 1.0 CG2 B:ILE305 4.9 18.4 1.0 N76 B:VKA406 5.0 24.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ B:F406 b:24.6 occ:1.00 F83 B:VKA406 0.0 24.6 1.0 C80 B:VKA406 1.4 21.9 1.0 F84 B:VKA406 2.2 21.7 1.0 F82 B:VKA406 2.2 19.6 1.0 C79 B:VKA406 2.4 20.1 1.0 O85 B:VKA406 2.8 21.8 1.0 C74 B:VKA406 3.0 19.1 1.0 C73 B:VKA406 3.2 16.1 1.0 O B:HOH614 3.3 38.6 1.0 O B:HOH513 3.4 38.3 1.0 C78 B:VKA406 3.5 21.5 1.0 CD2 B:LEU321 3.8 19.6 1.0 C75 B:VKA406 4.4 21.2 1.0 O B:HOH598 4.6 27.8 1.0 OE2 B:GLU322 4.6 22.5 0.6 N72 B:VKA406 4.6 18.4 1.0 C77 B:VKA406 4.6 23.1 1.0 CD1 B:LEU321 4.7 21.2 1.0 CD1 B:ILE305 4.8 21.2 1.0 CG B:LEU321 4.9 19.1 1.0 N76 B:VKA406 5.0 24.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Protac MS33 in Complex with the Wd Repeat- Containing Protein 5 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ B:F406 b:21.7 occ:1.00 F84 B:VKA406 0.0 21.7 1.0 C80 B:VKA406 1.4 21.9 1.0 F82 B:VKA406 2.2 19.6 1.0 F83 B:VKA406 2.2 24.6 1.0 C79 B:VKA406 2.4 20.1 1.0 C74 B:VKA406 2.9 19.1 1.0 C73 B:VKA406 3.0 16.1 1.0 O85 B:VKA406 3.1 21.8 1.0 CB B:SER49 3.5 17.2 1.0 C78 B:VKA406 3.5 21.5 1.0 C70 B:VKA406 3.6 17.2 1.0 CA B:SER49 3.8 18.4 1.0 C69 B:VKA406 3.8 15.7 1.0 N72 B:VKA406 3.9 18.4 1.0 CG1 B:ILE305 4.0 21.7 1.0 CD1 B:ILE305 4.2 21.2 1.0 C75 B:VKA406 4.3 21.2 1.0 CD2 B:LEU321 4.4 19.6 1.0 O B:SER49 4.4 16.7 1.0 CG2 B:ILE305 4.6 18.4 1.0 C B:SER49 4.6 16.1 1.0 O B:HOH598 4.7 27.8 1.0 C77 B:VKA406 4.7 23.1 1.0 N65 B:VKA406 4.8 14.1 1.0 CB B:ILE305 4.8 17.4 1.0 OG B:SER49 4.8 17.1 1.0 C61 B:VKA406 4.8 18.3 1.0 N B:SER49 4.8 18.1 1.0 N76 B:VKA406 5.0 24.4 1.0 O B:SER91 5.0 17.6 1.0 O B:VAL48 5.0 20.5 1.0

X.Yu, D.Li, J.Kottur, Y.Shen, H.S.Kim, K.-S.Park, Y.-H.Tsai, W.Gong, J.Wang, K.Suzuki, J.Parker, L.Herring, H.Kaniskan, L.Cai, R.Jain, J.Liu, A.K.Aggarwal, G.G.Wang, J.Jin. A Selective WDR5 Degrader Inhibits Acute Myeloid Leukemia in Patient-Derived Mouse Models Sci Transl Med 2021.
ISSN: ESSN 1946-6242
DOI: 10.1126/SCITRANSLMED.ABJ1578