Zinc in PDB 6u9m: MLL1 Set N3861I/Q3867L Bound to Inhibitor 16 (Tc-5109)

All present enzymatic activity of MLL1 Set N3861I/Q3867L Bound to Inhibitor 16 (Tc-5109):
2.1.1.43;

The structure of MLL1 Set N3861I/Q3867L Bound to Inhibitor 16 (Tc-5109), PDB code: 6u9m 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)	47.47 / 2.05
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	54.810, 54.810, 105.827, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 25.2

The binding sites of Zinc atom in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 16 (Tc-5109) (pdb code 6u9m). 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 16 (Tc-5109), PDB code: 6u9m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 16 (Tc-5109)


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 16 (Tc-5109) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4001 b:39.1 occ:1.00 SG A:CYS3909 2.2 52.9 1.0 SG A:CYS3959 2.3 40.5 1.0 SG A:CYS3957 2.4 43.0 1.0 SG A:CYS3964 2.5 43.9 1.0 CB A:CYS3909 3.3 48.6 1.0 CB A:CYS3959 3.4 36.8 1.0 CB A:CYS3957 3.5 39.0 1.0 CB A:CYS3964 3.5 40.4 1.0 N A:CYS3909 3.7 45.9 1.0 CA A:CYS3964 3.9 40.5 1.0 N A:CYS3959 4.1 36.3 1.0 CA A:CYS3909 4.1 47.4 1.0 N A:ARG3965 4.1 41.0 1.0 CA A:CYS3959 4.3 36.7 1.0 O A:HOH4135 4.4 28.0 1.0 C A:CYS3964 4.5 44.4 1.0 NE2 A:HIS3907 4.5 40.4 1.0 H5 A:Q2M4002 4.5 29.8 0.0 CD2 A:HIS3907 4.5 40.3 1.0 N A:LYS3966 4.6 39.3 1.0 CA A:CYS3957 4.7 37.8 1.0 C A:SER3908 4.7 44.5 1.0 C A:CYS3957 4.7 38.8 1.0 N A:GLY3960 4.8 36.9 1.0 CA A:SER3908 4.9 36.9 1.0 O A:CYS3957 4.9 38.3 1.0 C A:CYS3959 4.9 41.0 1.0

Zinc binding site 2 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 16 (Tc-5109)


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 16 (Tc-5109) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4001 b:38.6 occ:1.00 SG B:CYS3959 2.3 38.8 1.0 SG B:CYS3909 2.3 57.8 1.0 SG B:CYS3957 2.4 43.8 1.0 SG B:CYS3964 2.6 43.1 1.0 CB B:CYS3909 3.3 53.5 1.0 CB B:CYS3959 3.3 35.1 1.0 CB B:CYS3957 3.4 39.8 1.0 CB B:CYS3964 3.6 39.6 1.0 N B:CYS3909 3.7 49.4 1.0 CA B:CYS3964 3.9 39.7 1.0 N B:CYS3959 3.9 34.4 1.0 CA B:CYS3909 4.1 51.9 1.0 N B:ARG3965 4.2 39.8 1.0 CA B:CYS3959 4.2 35.0 1.0 NE2 B:HIS3907 4.4 40.8 1.0 O B:HOH4162 4.4 39.9 1.0 CD2 B:HIS3907 4.4 40.8 1.0 H5 B:Q2M4003 4.4 26.6 0.0 C B:CYS3964 4.5 43.8 1.0 N B:LYS3966 4.6 38.6 1.0 CA B:CYS3957 4.6 38.5 1.0 C B:SER3908 4.6 46.0 1.0 C B:CYS3957 4.6 38.8 1.0 N B:GLY3960 4.7 35.7 1.0 CA B:SER3908 4.8 38.9 1.0 O B:CYS3957 4.9 39.1 1.0 C B:CYS3959 4.9 40.1 1.0 N B:ASN3958 4.9 31.9 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