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7ty2

Crystal Structure of SETD2 Bound to an Indole-based Inhibitor

Method: X-RAY DIFFRACTION Dmax: 69.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase SETD2

Homo sapiens

UniProt Q9BYW2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1434–1711 Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 KS6 N-[(1R,3S)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M HEPES 7.5, 18% w/v PEG 2000 MME Resolution 2.44 Å R-free 0.270

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7TY2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2A7O Solution Structure of the hSet2/HYPB SRI domain Deposited 2005-07-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1954–2061（108 aa） Fragment：Set2 Rpb1-interacting (SRI) domain, HSET2/HYBP SRI domain, residues 1954-2061
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient
NMR sample composition U-15N (random labeling) HYPB, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition U-95% 13C, U-98% 15N labeled HYPB, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition Residue selective labeling with 15N-lysine HYPB, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition U-95% 13C, U-98% 15N HYPB, 100% D2O | 100% D2O
NMR sample composition Unlabeled HYPB,100% D2O | 100% D2O
NMR sample composition 10% 13C (fractional labeling) HYPB,100% D2O | 100% D2O
Resolution not provided
2MDC Solution structure of the WW domain of HYPB Deposited 2013-09-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2385–2430（46 aa） Fragment：UNP residues 2385- 2430
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition 500 mM [U-99% 13C; U-99% 15N] H2O-1, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MDI Solution structure of the PP2WW mutant (KPP2WW) of HYPB Deposited 2013-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2377–2430（54 aa） Fragment：UNP residues 2377-2430
Mutation：K11A, P12A, K13A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition 500 uM [U-99% 13C; U-99% 15N] KPP2WW-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 5%(w/v) sodium azide-4, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MDJ Solution structure of WW domain with polyproline stretch (PP2WW) of HYPB Deposited 2013-09-11 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2377–2430（54 aa） Fragment：UNP residues 2377-2430
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition 500uM [U-99% 13C; U-99% 15N] PP2WW-1, 20mM sodium phosphate-2, 50mM sodium chloride-3, 0.05%(w/v) sodium azide-4, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
4FMU Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF Deposited 2012-06-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa）
Not recorded ZN ZINC ION × 3 0UM (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid × 1 UNX UNKNOWN LIGAND × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG4000, 10% isoprpanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.235
4H12 The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine Deposited 2012-09-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa） Fragment：methyltransferase domain (UNP residues 1434-1711)
Not recorded ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1 uL protein (1:10 molar ratio of SETD2:AdoMet) + 1 uL reservoir solution (30% PEG2000 MME, 0.1 M potassium thiocyanate), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.06 Å R-free 0.249
5JJY Crystal structure of SETD2 bound to histone H3.3 K36M peptide Deposited 2016-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1434–1711（278 aa） Fragment：catalytic domain, UNP residues 1434-1711
Not recorded ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Resolution 2.05 Å R-free 0.213
5JLB Crystal structure of SETD2 bound to histone H3.3 K36I peptide Deposited 2016-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1434–1711（278 aa） Fragment：catalytic domain, UNP residues 1434-1711
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 3 GOL GLYCEROL × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Resolution 1.50 Å R-free 0.190
5JLE Crystal structure of SETD2 bound to SAH Deposited 2016-04-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa） Fragment：catalytic domain, UNP residues 1434-1711
Not recorded ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M KSCN, 30% PEG2000mme
Resolution 2.40 Å R-free 0.250
5LSS Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76H [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-propyl-azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M KSCN, 31.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7
Resolution 1.79 Å R-free 0.226
5LSX Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 76O [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, pH 7.3, 0.1MKSCN, 25-30%MPEG2000
Resolution 2.90 Å R-free 0.280
5LSY Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76M [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(2-methylpropyl)azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000
Resolution 1.62 Å R-free 0.215
5LSZ Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 SCN THIOCYANATE ION × 2 76K [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(3-oxidanylpropyl)azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes pH7.3, 0.1MKSCN, 25-30%MPEG2000
Resolution 1.62 Å R-free 0.201
5LT6 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76J [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000.
Resolution 2.05 Å R-free 0.231
5LT6 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76J [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000.
Resolution 2.05 Å R-free 0.231
5LT7 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa）
Not recorded ZN ZINC ION × 3 SCN THIOCYANATE ION × 2 76L [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-[(2~{R})-2-oxidanylpropyl]azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000
Resolution 1.51 Å R-free 0.192
5LT8 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1433–1711（279 aa）
Not recorded ZN ZINC ION × 3 SFG SINEFUNGIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES, PH7.3, 0.1MKSCN, 25-30%MPEG2000
Resolution 1.57 Å R-free 0.216
5V21 Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1435–1711（277 aa） Fragment：SET domain (UNP residues 1435-1711)
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M KSCN, 24% (v/v) PEG 2000 MME
Resolution 2.42 Å R-free 0.269
5V22 Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAH Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1435–1711（277 aa） Fragment：SET domain (UNP residues 1435-1711)
Not recorded ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M KSCN, 24% (v/v) PEG 2000 MME
Resolution 2.40 Å R-free 0.257
6J9J crystal structure of SESTD2 in complex with H3.3S31phK36M peptide Deposited 2019-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1447–1703（257 aa）
Not recorded ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M potassium thiocyanate, 0.1M Bis-Tris propane,20% PEG 3350
Resolution 1.78 Å R-free 0.206
6VDB SETD2 in complex with a H3-variant super-substrate peptide Deposited 2019-12-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1433–1711（279 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 20 ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M KSCN, 0.1 M Tris-HCl pH 8.5, and 26% PEG 3350
Resolution 2.30 Å R-free 0.263
7EA8 Human SETD2 bound to a nucleosome containing oncohistone mutations Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain L 1452–1696（245 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7EVR Crystal structure of hnRNP L RRM2 in complex with SETD2 Deposited 2021-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2167–2192（26 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Potassium/Sodium phosphate, pH 7.5
Resolution 1.80 Å R-free 0.198
7EVR Crystal structure of hnRNP L RRM2 in complex with SETD2 Deposited 2021-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2167–2192（26 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Potassium/Sodium phosphate, pH 7.5
Resolution 1.80 Å R-free 0.198
7EVS Crystal structure of hnRNP LL RRM2 in complex with SETD2 Deposited 2021-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2180–2192（13 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3M Ammonium Sulfate, 20% PEG 4000
Resolution 1.60 Å R-free 0.204
7EVS Crystal structure of hnRNP LL RRM2 in complex with SETD2 Deposited 2021-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2180–2192（13 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3M Ammonium Sulfate, 20% PEG 4000
Resolution 1.60 Å R-free 0.204
7LZB Crystal Structure of SETD2 bound to Compound 2 Deposited 2021-03-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YJ1 N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide × 1 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1M Tris pH 7.8, 25% w/v PEG 2000 MME
Resolution 2.28 Å R-free 0.264
7LZD Crystal Structure of SETD2 bound to Compound 35 Deposited 2021-03-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YHY N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 9 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M HEPES pH 7.5, 24% w/v PEG 2000 MME
Resolution 1.80 Å R-free 0.218
7LZF Crystal Structure of SETD2 bound to Compound 57 Deposited 2021-03-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YHV 4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl)(methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME
Resolution 2.47 Å R-free 0.263
7TY3 Crystal Structure of SETD2 Bound to an Indole-based Inhibitor Deposited 2022-02-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1434–1711（278 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 KRF N-[(1R,3R)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME
Resolution 2.30 Å R-free 0.270
8Q5P Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from human tyrosine kinase ACK1 Deposited 2023-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M TRIS pH 8.5, 16%w/v PEG 10000
Resolution 1.81 Å R-free 0.246
8RZU Structure of human SETD2 L1609P mutant in complex with SAM and H3K36M peptide Deposited 2024-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1433–1711（279 aa）
Mutation：L1609P ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；32% w/v PEG 4K, 100mM Tris, 800mM LiCl, pH 8.5
Resolution 2.19 Å R-free 0.264
9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain l 1435–2564（1130 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain l 1435–2564（1130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain l 1452–2040（589 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain l 1435–2564（1130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9G4A Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide Deposited 2024-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1433–1711（279 aa）
Mutation：T1663M ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；32% w/v PEG 4K, 100mM Tris, 800mM LiCl
Resolution 1.65 Å R-free 0.241
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain O 1435–2564（1130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9HGG SETD2 peptide bound to SPOP MATH domain Deposited 2024-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1363–1379（17 aa）
Not recorded MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5
Resolution 1.90 Å R-free 0.256
9RTN State 2 MAP 2 SPT6 with SETD2 Deposited 2025-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain O 1435–2564（1130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain O 1435–2564（1130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZD State 3 MAP 2 SPT6 with SETD2 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain O 1435–2564（1130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain O 1435–2564（1130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain O 1435–2564（1130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain O 1435–2564（1130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å

42 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SETD2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–278； UniProt 1434–1711

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7ty2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ty2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ty2
Deposition date deposition_date2022-02-11
Structure title titleCrystal Structure of SETD2 Bound to an Indole-based Inhibitor
Keywords keywordshistone-lysine N-methyltransferase, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.06 Å
Radius of gyration Rg (electron density) rg_electron18.97 Å
Forward intensity I(0) i015818500.00
Molecular weight molecular_weight28054.0 kDa
Excluded volume excluded_volume34281 ų
Envelope volume envelope_volume41851 ų
Hydration-shell volume shell_volume18682 ų
Envelope diameter envelope_diameter72.3 Å
Shell Rg shell_rg25.30 Å
Envelope Rg envelope_rg19.57 Å
Shape Rg shape_rg18.90 Å
Total Rg total_rg20.06 Å
Total atoms total_atoms1947
Residues n_residues234
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.7 Å
Rg (real space) rg_real20.02 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real1.5820e+07
I(0) uncertainty (real space) i0_real_error2.3650e+05
Rg (reciprocal space) rg_reciprocal20.03 Å
I(0) (reciprocal space) i0_reciprocal15820000.0000
Solution quality estimate total_estimate0.8692
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9 Å
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2646000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.782; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)