Zinc in PDB 7lzf: Crystal Structure of SETD2 Bound to Compound 57

All present enzymatic activity of Crystal Structure of SETD2 Bound to Compound 57:
2.1.1.359;

The structure of Crystal Structure of SETD2 Bound to Compound 57, PDB code: 7lzf was solved by N.A.Farrow, P.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.69 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.91, 76.648, 76.186, 90, 90, 90
R / Rfree (%)	21.6 / 26.3

The structure of Crystal Structure of SETD2 Bound to Compound 57 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of SETD2 Bound to Compound 57 (pdb code 7lzf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SETD2 Bound to Compound 57, PDB code: 7lzf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SETD2 Bound to Compound 57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SETD2 Bound to Compound 57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:60.8 occ:1.00 SG A:CYS1499 2.3 62.0 1.0 SG A:CYS1520 2.3 59.5 1.0 SG A:CYS1501 2.3 68.2 1.0 SG A:CYS1516 2.3 57.5 1.0 CB A:CYS1499 3.2 67.4 1.0 CB A:CYS1516 3.3 60.1 1.0 CB A:CYS1501 3.3 70.1 1.0 CB A:CYS1520 3.3 60.3 1.0 ZN A:ZN1802 3.6 56.3 1.0 CA A:CYS1516 3.8 61.2 1.0 CA A:CYS1520 4.0 61.3 1.0 SG A:CYS1529 4.1 52.1 1.0 N A:CYS1501 4.3 71.8 1.0 CA A:CYS1501 4.4 73.0 1.0 SG A:CYS1533 4.6 59.0 1.0 CA A:CYS1499 4.7 71.6 1.0 N A:CYS1516 4.7 61.9 1.0 N A:LEU1521 4.7 66.0 1.0 C A:CYS1520 4.8 63.8 1.0 ND2 A:ASN1535 4.9 69.0 1.0 C A:CYS1516 4.9 60.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SETD2 Bound to Compound 57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SETD2 Bound to Compound 57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:56.3 occ:1.00 SG A:CYS1539 2.3 57.6 1.0 SG A:CYS1529 2.3 52.1 1.0 SG A:CYS1533 2.3 59.0 1.0 SG A:CYS1516 2.3 57.5 1.0 CB A:CYS1529 3.1 52.5 1.0 CB A:CYS1539 3.4 59.6 1.0 CB A:CYS1516 3.4 60.1 1.0 CB A:CYS1533 3.5 60.4 1.0 ZN A:ZN1801 3.6 60.8 1.0 SG A:CYS1499 4.2 62.0 1.0 CA A:CYS1539 4.4 59.5 1.0 CB A:ASN1541 4.5 48.6 1.0 CA A:CYS1529 4.6 52.0 1.0 SG A:CYS1520 4.7 59.5 1.0 CA A:CYS1533 4.8 61.4 1.0 CA A:CYS1516 4.8 61.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SETD2 Bound to Compound 57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SETD2 Bound to Compound 57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:58.2 occ:1.00 SG A:CYS1631 2.3 55.4 1.0 SG A:CYS1678 2.3 53.9 1.0 SG A:CYS1680 2.3 59.4 1.0 SG A:CYS1685 2.3 66.5 1.0 CB A:CYS1631 3.3 56.9 1.0 CB A:CYS1678 3.4 54.9 1.0 CB A:CYS1685 3.4 65.6 1.0 CB A:CYS1680 3.4 60.1 1.0 CA A:CYS1685 3.7 67.1 1.0 N A:CYS1631 3.9 56.2 1.0 N A:CYS1680 4.1 58.8 1.0 CA A:CYS1631 4.2 57.9 1.0 N A:ARG1686 4.2 66.1 1.0 CA A:CYS1680 4.3 60.2 1.0 NE2 A:HIS1629 4.3 51.1 1.0 C A:CYS1685 4.4 66.7 1.0 CD2 A:HIS1629 4.5 50.0 1.0 CA A:CYS1678 4.6 56.4 1.0 C A:CYS1678 4.6 58.2 1.0 O A:CYS1678 4.7 58.2 1.0 N A:GLY1687 4.7 61.5 1.0 C A:CYS1680 4.9 61.3 1.0 N A:GLY1681 4.9 63.0 1.0 N A:CYS1685 4.9 68.2 1.0 C A:SER1630 4.9 54.6 1.0

J.W.Lampe, J.S.Alford, P.A.Boriak-Sjodin, D.Brach, K.Cosmopoulos, K.W.Duncan, S.T.Eckley, M.A.Foley, D.M.Harvey, V.Motwani, M.J.Munchhof, A.Raimondi, T.V.Riera, C.Tang, M.J.Thomenius, J.Totman, N.A.Farrow. Discovery of A First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable For Preclinical Studies Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00272