Zinc in PDB 7lzb: Crystal Structure of SETD2 Bound to Compound 2

All present enzymatic activity of Crystal Structure of SETD2 Bound to Compound 2:
2.1.1.359;

The structure of Crystal Structure of SETD2 Bound to Compound 2, PDB code: 7lzb 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)	54.63 / 2.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.545, 76.751, 77.775, 90, 90, 90
R / Rfree (%)	20.5 / 26.4

The binding sites of Zinc atom in the Crystal Structure of SETD2 Bound to Compound 2 (pdb code 7lzb). 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 2, PDB code: 7lzb:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:65.7 occ:1.00 SG A:CYS1499 2.3 62.5 1.0 SG A:CYS1501 2.3 73.8 1.0 SG A:CYS1520 2.3 66.4 1.0 SG A:CYS1516 2.4 59.0 1.0 CB A:CYS1516 3.3 65.8 1.0 CB A:CYS1501 3.3 80.8 1.0 CB A:CYS1520 3.3 69.0 1.0 CB A:CYS1499 3.3 69.8 1.0 ZN A:ZN1802 3.7 59.9 1.0 CA A:CYS1516 3.8 65.3 1.0 CA A:CYS1520 4.0 63.9 1.0 N A:CYS1501 4.1 86.1 1.0 SG A:CYS1529 4.3 57.7 1.0 CA A:CYS1501 4.3 83.6 1.0 N A:CYS1516 4.6 66.2 1.0 N A:LEU1521 4.7 67.5 1.0 CA A:CYS1499 4.7 72.2 1.0 C A:CYS1520 4.8 63.8 1.0 SG A:CYS1533 4.8 62.7 1.0 N A:GLU1500 4.8 77.2 1.0 C A:CYS1516 4.9 69.8 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:59.9 occ:1.00 SG A:CYS1533 2.3 62.7 1.0 SG A:CYS1516 2.3 59.0 1.0 SG A:CYS1539 2.3 58.4 1.0 SG A:CYS1529 2.3 57.7 1.0 CB A:CYS1529 3.2 53.1 1.0 CB A:CYS1516 3.3 65.8 1.0 CB A:CYS1539 3.5 59.3 1.0 CB A:CYS1533 3.5 60.8 1.0 ZN A:ZN1801 3.7 65.7 1.0 SG A:CYS1499 4.2 62.5 1.0 CA A:CYS1539 4.4 57.8 1.0 CB A:ASN1541 4.4 52.3 1.0 CA A:CYS1529 4.6 54.5 1.0 SG A:CYS1520 4.6 66.4 1.0 CA A:CYS1516 4.7 65.3 1.0 CA A:CYS1533 4.8 61.4 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:62.1 occ:1.00 SG A:CYS1680 2.3 58.0 1.0 SG A:CYS1678 2.3 59.9 1.0 SG A:CYS1685 2.3 66.6 1.0 SG A:CYS1631 2.3 58.2 1.0 CB A:CYS1680 3.3 62.3 1.0 CB A:CYS1685 3.3 68.6 1.0 CB A:CYS1678 3.3 55.2 1.0 CB A:CYS1631 3.4 62.6 1.0 CA A:CYS1685 3.7 68.2 1.0 N A:CYS1631 3.8 67.8 1.0 N A:CYS1680 4.1 59.0 1.0 N A:ARG1686 4.2 67.3 1.0 CA A:CYS1680 4.2 59.0 1.0 NE2 A:HIS1629 4.2 54.4 1.0 CA A:CYS1631 4.2 66.3 1.0 C A:CYS1685 4.3 67.4 1.0 CD2 A:HIS1629 4.4 56.2 1.0 CA A:CYS1678 4.5 57.5 1.0 N A:GLY1687 4.6 64.8 1.0 C A:CYS1678 4.6 56.4 1.0 O A:CYS1678 4.8 56.8 1.0 C A:SER1630 4.9 59.6 1.0 C A:CYS1680 4.9 63.3 1.0 N A:CYS1685 4.9 69.8 1.0 N A:GLY1681 5.0 66.5 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