Histone-lysine N-methyltransferase EHMT1
Homo sapiens
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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 982–1266 Chain B； UniProt 982–1266 | Fragment：residues 982-1266 | SAM S-ADENOSYLMETHIONINE × 2 90P N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine × 2 ZN ZINC ION × 8 CL CHLORIDE ION × 3 UNX UNKNOWN LIGAND × 13 DMS DIMETHYL SULFOXIDE × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6 | Resolution 1.74 Å R-free 0.197 |
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 5V9J | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2IGQ Human euchromatic histone methyltransferase 1 Deposited 2006-09-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal domain, residues 951-1235
Chain B
951–1235（285 aa）
Fragment：C-terminal domain, residues 951-1235
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；20% PEG 4K, 10% Isoproponol, 0.1M Hepes 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.00 Å R-free 0.237 |
| 2RFI Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide Deposited 2007-09-30 | 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
951–1235（285 aa）
Fragment：Catalytic domain: Residues 951-1235
|
Not recorded | ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.59 Å R-free 0.220 |
| 2RFI Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide Deposited 2007-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
951–1235（285 aa）
Fragment：Catalytic domain: Residues 951-1235
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.59 Å R-free 0.220 |
| 2RFI Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide Deposited 2007-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
951–1235（285 aa）
Fragment：Catalytic domain: Residues 951-1235
Chain B
951–1235（285 aa）
Fragment：Catalytic domain: Residues 951-1235
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.59 Å R-free 0.220 |
| 3B7B EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1) Deposited 2007-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
734–968（235 aa）
Fragment：Ankyrin repeat domains 2-7
|
Not recorded | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；1.5-2.0 M Lithium Sulfate, 1-4% Peg 400 or 550, 0.1 M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 2.99 Å R-free 0.261 |
| 3B7B EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1) Deposited 2007-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
734–968（235 aa）
Fragment：Ankyrin repeat domains 2-7
|
Not recorded | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；1.5-2.0 M Lithium Sulfate, 1-4% Peg 400 or 550, 0.1 M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 2.99 Å R-free 0.261 |
| 3FPD G9a-like protein lysine methyltransferase inhibition by BIX-01294 Deposited 2009-01-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
975–1235（261 aa）
Fragment：UNP residues 975-1235, SET domain
Chain B
975–1235（261 aa）
Fragment：UNP residues 975-1235, SET domain
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 Q4A N-(1-benzylpiperidin-4-yl)-6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)quinazolin-4-amine × 2 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；289 K；0.1 M HEPES pH 7.5, 18-20 % polyethylene glycol 4000 and 7-10 % isopropanol, in the absence or presence of DMSO (6-36%), VAPOR DIFFUSION, temperature 289K
|
Resolution 2.40 Å R-free 0.262 |
| 3HNA Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide Deposited 2009-05-30 | 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
951–1235（285 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；300 K；20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.50 Å R-free 0.193 |
| 3HNA Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide Deposited 2009-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
951–1235（285 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；300 K；20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.50 Å R-free 0.193 |
| 3HNA Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide Deposited 2009-05-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
951–1235（285 aa）
Chain B
951–1235（285 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；300 K；20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.50 Å R-free 0.193 |
| 3MO0 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 2 ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.78 Å R-free 0.306 |
| 3MO0 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.78 Å R-free 0.306 |
| 3MO0 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 Deposited 2010-04-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal SET domain
Chain B
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 3 ZN ZINC ION × 10 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.78 Å R-free 0.306 |
| 3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.49 Å R-free 0.248 |
| 3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.49 Å R-free 0.248 |
| 3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.49 Å R-free 0.248 |
| 3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.49 Å R-free 0.248 |
| 3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal SET domain
Chain B
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 8 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.49 Å R-free 0.248 |
| 3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
951–1235（285 aa）
Fragment：C-terminal SET domain
Chain D
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 8 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.49 Å R-free 0.248 |
| 3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.14 Å R-free 0.233 |
| 3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.14 Å R-free 0.233 |
| 3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.14 Å R-free 0.233 |
| 3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.14 Å R-free 0.233 |
| 3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
951–1235（285 aa）
Fragment：C-terminal SET domain
Chain B
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 8 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.14 Å R-free 0.233 |
| 3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
951–1235（285 aa）
Fragment：C-terminal SET domain
Chain D
951–1235（285 aa）
Fragment：C-terminal SET domain
|
Not recorded | ZN ZINC ION × 8 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.14 Å R-free 0.233 |
| 3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13 | 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
982–1266（285 aa）
Fragment：unp residues 982-1266
|
Not recorded | ZN ZINC ION × 4 SFG SINEFUNGIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 3.05 Å R-free 0.248 |
| 3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
982–1266（285 aa）
Fragment：unp residues 982-1266
|
Not recorded | ZN ZINC ION × 4 SFG SINEFUNGIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 3.05 Å R-free 0.248 |
| 3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
982–1266（285 aa）
Fragment：unp residues 982-1266
Chain B
982–1266（285 aa）
Fragment：unp residues 982-1266
|
Not recorded | ZN ZINC ION × 8 SFG SINEFUNGIN × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 3.05 Å R-free 0.248 |
| 3SWC GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide Deposited 2011-07-13 | 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
982–1266（285 aa）
Fragment：unp residues 982-1266
|
Not recorded | ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.33 Å R-free 0.227 |
| 3SWC GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide Deposited 2011-07-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
982–1266（285 aa）
Fragment：unp residues 982-1266
|
Not recorded | ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.33 Å R-free 0.227 |
| 3SWC GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide Deposited 2011-07-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
982–1266（285 aa）
Fragment：unp residues 982-1266
Chain B
982–1266（285 aa）
Fragment：unp residues 982-1266
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.33 Å R-free 0.227 |
| 4I51 Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A Deposited 2012-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
982–1266（285 aa）
Chain B
982–1266（285 aa）
|
Mutation：Y1211A Mutation：Y1211A | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 GOL GLYCEROL × 3 UNX UNKNOWN LIGAND × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；10% ISOPROPANOL, 20% PEG4000; 0.1M HEPES PH7.5, VAPOR DIFFUSION HANGING DROP, TEMPERATURE 297K
|
Resolution 1.90 Å R-free 0.195 |
| 5TTG Crystal structure of catalytic domain of GLP with MS012 Deposited 2016-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
982–1266（285 aa）
Fragment：UNP residues 879-1159
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 7KZ N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6
|
Resolution 1.66 Å R-free 0.192 |
| 5TTG Crystal structure of catalytic domain of GLP with MS012 Deposited 2016-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
982–1266（285 aa）
Fragment：UNP residues 879-1159
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 7KZ N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 9 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6
|
Resolution 1.66 Å R-free 0.192 |
| 5TUZ Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124 Deposited 2016-11-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1006–1266（261 aa）
Fragment：UNP residues 1006-1266
Chain B
1006–1266（261 aa）
Fragment：UNP residues 1006-1266
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 7L6 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；290 K；20% PEG 20,000, 2% (v/v) 1,4-Dioxane, 0.1 M Bicine (pH 9.0)
|
Resolution 1.95 Å R-free 0.201 |
| 5VSD Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 13 Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1006–1266（261 aa）
Fragment：GLP catalytic SET-domain residues 1006-1266
Chain B
1006–1266（261 aa）
Fragment：GLP catalytic SET-domain residues 1006-1266
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 9HJ 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine × 2 DIO 1,4-DIETHYLENE DIOXIDE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；290 K；7 % PEG 20K, 1.4% v/v 1,4-Dioxane, 10% glycerol, 0.07 M Bicine, pH 9.0
|
Resolution 1.85 Å R-free 0.235 |
| 5VSF Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 17 Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1006–1266（261 aa）
Fragment：GLP catalytic SET-domain residues 1006-1266
Chain B
1006–1266（261 aa）
Fragment：GLP catalytic SET-domain residues 1006-1266
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 9HG N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine × 2 DIO 1,4-DIETHYLENE DIOXIDE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；290 K；10 % PEG 20K, 1.4% v/v 1,4-Dioxane, 10% glycerol, 0 0.1 M Bicine, pH 9.0
|
Resolution 1.70 Å R-free 0.185 |
| 6BY9 Crystal structure of EHMT1 Deposited 2017-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
672–999（328 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS pH6.5,3.0M NaCl
|
Resolution 2.30 Å R-free 0.238 |
| 6MBO GLP Methyltransferase with Inhibitor EML741-P212121 Crystal Form Deposited 2018-08-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1006–1266（261 aa）
Chain B
1006–1266（261 aa）
|
Not recorded | JDG 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine × 4 ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 EDO 1,2-ETHANEDIOL × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；15% PEG 4000, 20% isopropanol and 100mM citrate (pH 5.5)
|
Resolution 1.59 Å R-free 0.194 |
| 6MBP GLP Methyltransferase with Inhibitor EML741- P3121 Crystal Form Deposited 2018-08-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1006–1266（261 aa）
Fragment：residues 1006-1266
Chain B
1006–1266（261 aa）
Fragment：residues 1006-1266
|
Not recorded | JDG 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine × 2 ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 EDO 1,2-ETHANEDIOL × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；15% PEG 4000, 20% isopropanol and 100mM citrate (pH 5.5)
|
Resolution 1.95 Å R-free 0.182 |
| 7T7M Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1) Deposited 2021-12-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
982–1266（285 aa）
Fragment：residues 982-1266
Chain D
982–1266（285 aa）
Fragment：residues 982-1266
|
Not recorded | ZN ZINC ION × 8 G4R N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)prop-2-enamide × 1 G5U N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290.15 K；0.2 Magnesium Formate, 15% w/v Polyethylene glycol 3350
|
Resolution 2.85 Å R-free 0.244 |
| 7T7M Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1) Deposited 2021-12-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
982–1266（285 aa）
Fragment：residues 982-1266
Chain C
982–1266（285 aa）
Fragment：residues 982-1266
|
Not recorded | ZN ZINC ION × 8 G4R N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)prop-2-enamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290.15 K；0.2 Magnesium Formate, 15% w/v Polyethylene glycol 3350
|
Resolution 2.85 Å R-free 0.244 |
| 8XPT The Crystal Structure of EHMT1 from Biortus. Deposited 2024-01-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
982–1266（285 aa）
Chain C
982–1266（285 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 25% PEG MME 5000
|
Resolution 3.35 Å R-free 0.262 |
| 8XPT The Crystal Structure of EHMT1 from Biortus. Deposited 2024-01-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
982–1266（285 aa）
Chain D
982–1266（285 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 25% PEG MME 5000
|
Resolution 3.35 Å R-free 0.262 |
| 9YKR Crystal structure of the GLP (EHMT1) SET domain in complex with SAM and TNG917 Deposited 2025-10-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1006–1266（261 aa）
Fragment：catalytic SET domain (UNP residues 1006-1266)
Chain B
1006–1266（261 aa）
Fragment：catalytic SET domain (UNP residues 1006-1266)
|
Not recorded | ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 A1CXM N~2~-[(7M)-6-fluoro-7-(2,5,6,7-tetrahydro-1H-azepin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]-N~4~,6-dimethylpyrimidine-2,4-diamine × 2 PEG DI(HYDROXYETHYL)ETHER × 4 SO4 SULFATE ION × 16 EDO 1,2-ETHANEDIOL × 21 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；298 K；30% PEG3350, 200 mM lithium sulfate, 100 mM Bis-Tris, pH 5.5
|
Resolution 1.38 Å R-free 0.154 |
21 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | EHMT1_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 3–287； UniProt 982–1266 Author chain B； PDBConstruct 3–287； UniProt 982–1266 |