Zinc in PDB 7ty2: Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor

All present enzymatic activity of Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor:
2.1.1.359;

The structure of Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor, PDB code: 7ty2 was solved by N.A.Farrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.693, 75.74, 75.923, 90, 90, 90
R / Rfree (%)	21.3 / 27

The structure of Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor (pdb code 7ty2). 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 An Indole-Based Inhibitor, PDB code: 7ty2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor


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 An Indole-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:79.0 occ:1.00 SG A:CYS1499 2.3 77.5 1.0 SG A:CYS1520 2.3 83.4 1.0 SG A:CYS1516 2.3 78.6 1.0 SG A:CYS1501 2.4 93.2 1.0 CB A:CYS1501 3.2 96.3 1.0 CB A:CYS1499 3.2 88.6 1.0 CB A:CYS1520 3.2 86.1 1.0 CB A:CYS1516 3.3 83.3 1.0 ZN A:ZN1802 3.7 72.0 1.0 CA A:CYS1516 3.7 82.6 1.0 CA A:CYS1520 3.9 82.4 1.0 N A:CYS1501 4.2 103.1 1.0 SG A:CYS1529 4.2 74.5 1.0 CA A:CYS1501 4.2 102.1 1.0 SG A:CYS1533 4.6 78.7 1.0 N A:CYS1516 4.6 82.1 1.0 CA A:CYS1499 4.6 90.0 1.0 C A:CYS1520 4.7 79.9 1.0 N A:LEU1521 4.7 76.9 1.0 C A:CYS1516 4.8 84.8 1.0 N A:GLU1500 5.0 104.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor


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 An Indole-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:72.0 occ:1.00 SG A:CYS1529 2.3 74.5 1.0 SG A:CYS1516 2.3 78.6 1.0 SG A:CYS1533 2.3 78.7 1.0 SG A:CYS1539 2.3 72.4 1.0 CB A:CYS1529 3.0 71.6 1.0 CB A:CYS1516 3.4 83.3 1.0 CB A:CYS1539 3.4 77.5 1.0 CB A:CYS1533 3.6 77.6 1.0 ZN A:ZN1801 3.7 79.0 1.0 SG A:CYS1499 4.1 77.5 1.0 CB A:ASN1541 4.4 65.7 1.0 CA A:CYS1539 4.4 78.8 1.0 CA A:CYS1529 4.4 69.6 1.0 SG A:CYS1520 4.7 83.4 1.0 CA A:CYS1516 4.8 82.6 1.0 ND2 A:ASN1541 4.8 68.8 1.0 CA A:CYS1533 4.8 77.4 1.0 N A:CYS1529 4.9 68.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SETD2 Bound to An Indole-Based Inhibitor


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 An Indole-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:70.3 occ:1.00 SG A:CYS1678 2.3 72.2 1.0 SG A:CYS1680 2.3 72.0 1.0 SG A:CYS1631 2.3 73.7 1.0 SG A:CYS1685 2.3 82.2 1.0 CB A:CYS1678 3.1 69.2 1.0 CB A:CYS1631 3.3 81.8 1.0 CB A:CYS1685 3.4 81.7 1.0 CB A:CYS1680 3.4 76.4 1.0 CA A:CYS1685 3.6 84.3 1.0 N A:CYS1631 3.9 85.1 1.0 N A:CYS1680 4.1 72.5 1.0 N A:ARG1686 4.2 82.6 1.0 CA A:CYS1631 4.2 83.2 1.0 CA A:CYS1680 4.3 74.1 1.0 C A:CYS1685 4.3 85.3 1.0 CA A:CYS1678 4.4 69.7 1.0 N A:GLY1687 4.5 81.3 1.0 OG A:SER1682 4.5 90.4 0.5 NE2 A:HIS1629 4.5 60.9 1.0 C A:CYS1678 4.6 69.1 1.0 CD2 A:HIS1629 4.6 58.1 1.0 N A:CYS1685 4.9 85.0 1.0 CB A:SER1682 4.9 90.7 0.5 N A:GLY1681 5.0 81.9 1.0 N A:PHE1679 5.0 68.7 1.0 C A:SER1630 5.0 80.2 1.0 CB A:SER1682 5.0 86.7 0.5

J.S.Alford, J.W.Lampe, D.Brach, R.Chesworth, K.Cosmopoulos, K.W.Duncan, S.T.Eckley, J.L.Kutok, A.Raimondi, T.V.Riera, B.Shook, C.Tang, J.Totman, N.A.Farrow. Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor For Clinical Studies. Acs Med.Chem.Lett. V. 13 1137 2022.
ISSN: ISSN 1948-5875
PubMed: 35859865
DOI: 10.1021/ACSMEDCHEMLETT.2C00167