Zinc in PDB 6u9r: MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140)

All present enzymatic activity of MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140):
2.1.1.43;

The structure of MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140), PDB code: 6u9r was solved by E.M.Petrunak, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.61 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	54.692, 54.692, 105.530, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.5

The structure of MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140) (pdb code 6u9r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140), PDB code: 6u9r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4001 b:43.9 occ:1.00 SG A:CYS3959 2.3 41.4 1.0 SG A:CYS3909 2.3 50.0 1.0 SG A:CYS3957 2.3 48.8 1.0 SG A:CYS3964 2.5 46.5 1.0 CB A:CYS3909 3.3 46.0 1.0 CB A:CYS3959 3.3 37.9 1.0 CB A:CYS3964 3.6 42.8 1.0 CB A:CYS3957 3.7 44.8 1.0 N A:CYS3909 3.7 44.6 1.0 CA A:CYS3964 4.0 42.7 1.0 N A:CYS3959 4.0 37.8 1.0 CA A:CYS3909 4.1 45.6 1.0 N A:ARG3965 4.2 42.3 1.0 CA A:CYS3959 4.2 37.9 1.0 O A:HOH4150 4.4 40.3 1.0 H6 A:Q2P4002 4.5 19.6 1.0 C A:CYS3964 4.5 45.9 1.0 N A:LYS3966 4.6 40.4 1.0 NE2 A:HIS3907 4.6 42.0 1.0 C A:SER3908 4.6 44.7 1.0 N A:GLY3960 4.7 37.1 1.0 C A:CYS3957 4.7 44.3 1.0 CD2 A:HIS3907 4.8 41.7 1.0 CA A:SER3908 4.8 37.5 1.0 CA A:CYS3957 4.8 43.7 1.0 O A:CYS3957 4.8 44.8 1.0 C A:CYS3959 4.9 41.8 1.0

Zinc binding site 2 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MLL1 Set N3861I/Q3867L Bound to Inhibitor 12 (Tc-5140) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4001 b:44.4 occ:1.00 SG B:CYS3959 2.3 42.1 1.0 SG B:CYS3957 2.3 49.1 1.0 SG B:CYS3909 2.3 50.0 1.0 SG B:CYS3964 2.5 45.6 1.0 CB B:CYS3959 3.3 38.9 1.0 CB B:CYS3909 3.4 46.2 1.0 CB B:CYS3964 3.5 41.8 1.0 CB B:CYS3957 3.7 44.9 1.0 N B:CYS3909 3.8 44.2 1.0 CA B:CYS3964 3.9 41.3 1.0 N B:CYS3959 4.0 38.6 1.0 CA B:CYS3959 4.2 39.0 1.0 CA B:CYS3909 4.3 45.7 1.0 N B:ARG3965 4.3 38.1 1.0 O B:HOH4157 4.3 38.7 1.0 H6 B:Q2P4002 4.5 19.6 1.0 C B:CYS3964 4.5 42.3 1.0 NE2 B:HIS3907 4.6 40.5 1.0 N B:LYS3966 4.6 37.8 1.0 N B:GLY3960 4.7 38.3 1.0 CD2 B:HIS3907 4.7 40.3 1.0 C B:CYS3957 4.7 43.8 1.0 C B:SER3908 4.8 43.5 1.0 CA B:CYS3957 4.8 43.7 1.0 O B:CYS3957 4.8 43.6 1.0 CA B:SER3908 4.9 36.4 1.0 C B:CYS3959 4.9 42.9 1.0

T.R.Chern, L.Liu, E.Petrunak, J.A.Stuckey, M.Wang, D.Bernard, H.Zhou, S.Lee, Y.Dou, S.Wang. Discovery of Potent Small-Molecule Inhibitors of Mll Methyltransferase. Acs Med.Chem.Lett. V. 11 1348 2020.
ISSN: ISSN 1948-5875
PubMed: 32551023
DOI: 10.1021/ACSMEDCHEMLETT.0C00229