Zinc in PDB 7ty3: 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: 7ty3 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)	43.13 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.092, 76.702, 75.461, 90, 90, 90
R / Rfree (%)	21.4 / 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 7ty3). 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: 7ty3:
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:64.5 occ:1.00 SG A:CYS1499 2.3 80.9 1.0 SG A:CYS1516 2.3 63.4 1.0 SG A:CYS1520 2.3 72.0 1.0 SG A:CYS1501 2.3 77.1 1.0 CB A:CYS1499 3.2 82.1 1.0 CB A:CYS1516 3.2 66.4 1.0 CB A:CYS1520 3.3 73.6 1.0 CB A:CYS1501 3.3 82.5 1.0 ZN A:ZN1802 3.6 54.8 1.0 CA A:CYS1516 3.7 67.0 1.0 CA A:CYS1520 4.0 73.2 1.0 SG A:CYS1529 4.2 58.8 1.0 N A:CYS1501 4.3 85.8 1.0 CA A:CYS1501 4.4 84.1 1.0 CA A:CYS1499 4.6 84.5 1.0 ND2 A:ASN1535 4.6 68.4 1.0 N A:CYS1516 4.7 67.8 1.0 SG A:CYS1533 4.7 63.2 1.0 C A:CYS1520 4.8 73.2 1.0 N A:GLU1500 4.9 85.3 1.0 C A:CYS1516 4.9 67.8 1.0 N A:LEU1521 4.9 72.9 1.0 C A:CYS1499 5.0 85.1 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:54.8 occ:1.00 SG A:CYS1516 2.3 63.4 1.0 SG A:CYS1539 2.3 59.3 1.0 SG A:CYS1533 2.4 63.2 1.0 SG A:CYS1529 2.4 58.8 1.0 CB A:CYS1529 3.1 56.1 1.0 CB A:CYS1516 3.3 66.4 1.0 CB A:CYS1533 3.4 64.9 1.0 CB A:CYS1539 3.4 60.9 1.0 ZN A:ZN1801 3.6 64.5 1.0 SG A:CYS1499 4.1 80.9 1.0 CA A:CYS1539 4.3 59.4 1.0 CB A:ASN1541 4.4 53.2 1.0 CA A:CYS1529 4.6 55.5 1.0 CA A:CYS1533 4.7 64.9 1.0 SG A:CYS1520 4.7 72.0 1.0 ND2 A:ASN1535 4.7 68.4 1.0 CA A:CYS1516 4.7 67.0 1.0 CB A:ASN1535 4.9 66.5 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:55.0 occ:1.00 SG A:CYS1678 2.3 58.7 1.0 SG A:CYS1680 2.3 63.7 1.0 SG A:CYS1631 2.3 59.6 1.0 SG A:CYS1685 2.4 71.3 1.0 CB A:CYS1685 3.3 72.8 1.0 CB A:CYS1631 3.3 62.1 1.0 CB A:CYS1680 3.4 63.2 1.0 CB A:CYS1678 3.4 59.7 1.0 CA A:CYS1685 3.6 72.5 1.0 N A:CYS1631 3.8 58.9 1.0 N A:ARG1686 4.1 70.9 1.0 CA A:CYS1631 4.2 60.1 1.0 N A:CYS1680 4.2 59.7 1.0 NE2 A:HIS1629 4.3 52.0 1.0 C A:CYS1685 4.3 71.5 1.0 CA A:CYS1680 4.3 61.7 1.0 CD2 A:HIS1629 4.5 50.7 1.0 N A:GLY1687 4.5 64.9 1.0 CA A:CYS1678 4.7 58.3 1.0 C A:CYS1678 4.8 57.9 1.0 N A:CYS1685 4.8 73.5 1.0 N A:GLY1681 4.8 65.6 1.0 C A:SER1630 4.8 57.5 1.0 O A:CYS1678 4.8 58.0 1.0 C A:CYS1680 5.0 63.1 1.0

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