7LZD: SETD2

Name: PDB 7LZD: Crystal Structure of SETD2 bound to Compound 35
Published: 2021-09-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal Structure of SETD2 bound to Compound 35. Determined by X-ray diffraction at 1.8 Å resolution. Released 22 Sept 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,177
Mol. weight: 33.58 kDa
Ligands: ZN, SAM, YHY
Released: 22 Sept 2021

Explore 7LZD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LZD contains 14 α-helices and 22 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	1448-1450	3	1
α-helix	1451-1455	5
α-helix	1457-1465	9
α-helix	1470-1472	3
β-strand	1474-1475	2	2
β-strand	1480-1481	2	3
α-helix	1501-1505	5
α-helix	1506-1511	6
α-helix	1513-1514	2
α-helix	1521-1524	4
β-strand	1527	1	4
α-helix	1536-1538	3
β-strand	1552-1556	5	1
β-strand	1562-1566	5	1
β-strand	1570	1	5
β-strand	1575-1578	4	4
β-strand	1582-1584	3	3
α-helix	1586-1598	13
β-strand	1606-1610	5	3
β-strand	1613-1616	4	3
β-strand	1620-1621	2	2
α-helix	1623-1626	4
α-helix	1627	1
β-strand	1628-1629	2	4
β-strand	1635-1642	8	4
β-strand	1645-1652	8	4
β-strand	1656	1	5
α-helix	1660	1
β-strand	1661-1662	2	1
β-strand	1663-1664	2	4
β-strand	1668	1	6
α-helix	1675-1676	2
β-strand	1677	1	7
α-helix	1678	1
β-strand	1688	1	7
β-strand	1691	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD2	A	protein	278	Homo sapiens	Q9BYW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7LZD_1 Histone-lysine N-methyltransferase SETD2 (chains A)
GETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRD
IKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVE
VILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDE
IIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGK
EAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
YHY	N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-car…	C23 H27 F N4 O	1

Water and common crystallization additives (EDO, DMS) are not listed.

Primary citation

Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies. Lampe, J.W., Alford, J.S., Boriak-Sjodin, P.A. et al. ACS Med Chem Lett (2021) 12:1539-1545. DOI 10.1021/acsmedchemlett.1c00272 · PubMed

Other PDB entries of the same protein (UniProt Q9BYW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
5LT7 1.51 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LT8 1.57 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVS 1.6 Å, Crystal structure of hnRNP LL RRM2 in complex with SETD2
5LSY 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LSZ 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
6J9J 1.78 Å, crystal structure of SESTD2 in complex with H3.3S31phK36M peptide
5LSS 1.79 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVR 1.8 Å, Crystal structure of hnRNP L RRM2 in complex with SETD2
8Q5P 1.81 Å, Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from…
9HGG 1.9 Å, SETD2 peptide bound to SPOP MATH domain

Browse structure collections

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