5dtm

Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide]

Method: X-RAY DIFFRACTION D_max: 101.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase, H3 lysine-79 specific

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–332	Not recorded	5F4 4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；1.0M K/Na tartrate 0.1M Hepes pH6.8	Resolution 2.20 Å R-free 0.199
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–332	Not recorded	5F4 4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；1.0M K/Na tartrate 0.1M Hepes pH6.8	Resolution 2.20 Å R-free 0.199

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 5DTM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NW3 Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase Deposited 2003-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa）	Not recorded	ACT ACETATE ION × 1 SO4 SULFATE ION × 2 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.50 Å R-free 0.246
2MV7 Solution NMR structure of DOT1L in complex with AF9 (DOT1L-AF9) Deposited 2014-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 877–900（24 aa） Fragment：UNP RESIDUES 877-900	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 750 uM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 uM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3QOW DOT1L Structure in complex with SAM Deposited 2011-02-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa） Fragment：UNP residues 1-416	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；2 M Ammonium Sulfate, 0.1 M Sodium Acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.192
3QOX DOT1L structure in complex with SAH Deposited 2011-02-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa） Fragment：UNP residues 1-416	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；2 M Ammonium Sulfate, 2 mM TCEP, 0.1 M Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.252
3SR4 Crystal Structure of Human DOT1L in Complex with a Selective Inhibitor Deposited 2011-07-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–351（351 aa） Fragment：CATALYTIC DOMAIN OF HDOT1L (UNP residues 1-351)	Not recorded	TT8 (2S)-2-azanyl-4-[[(2S,3S,4R,5R)-5-[6-(methylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；295 K；PROTEIN SOLUTION: 20 mM Tris, pH 8.0, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 3 mM inhibitor, 3 mM TCEP. RESERVOIR SOLUTION: 0.1 M HAC, pH 5.3, 1.25-1.7 M (NH4)2SO4. , VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.274
3SX0 Crystal structure of Dot1l in complex with a brominated SAH analog Deposited 2011-07-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa） Fragment：sequence database residues 1-420	Not recorded	SX0 (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(4-amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name) × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；291 K；1.5 M ammonium sulfate, 0.1 M sodium acetate, 0.0015 M ligand, pH 4.6, vapor diffusion, temperature 291K, VAPOR DIFFUSION	Resolution 2.28 Å R-free 0.228
3UWP Crystal structure of Dot1l in complex with 5-iodotubercidin Deposited 2011-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa） Fragment：UNP Residues 1-420	Not recorded	5ID (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 IOD IODIDE ION × 2 NA SODIUM ION × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；291 K；3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, temperature 291K	Resolution 2.05 Å R-free 0.223
4EK9 Crystal structure of DOT1L in complex with EPZ000004 Deposited 2012-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa） Fragment：UNP residues 1-416	Not recorded	EP4 5'-deoxy-5'-(dimethylamino)adenosine × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.263
4EKG Crystal Structure of DOT1L in Complex with EPZ003696 Deposited 2012-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa） Fragment：UNP residues 1-416	Not recorded	0QJ 5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(methyl)amino]-5'-deoxyadenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.2, soaking the compound into cross-linked DOT1L-SAM crystal, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.261
4EKI Crystal Structure of DOT1L in complex with EPZ004777 Deposited 2012-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa） Fragment：UNP residues 1-416	Not recorded	0QK 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.2, compound soaked into cross-linked DOT1L-SAM crystal, temperature 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.85 Å R-free 0.262
4EQZ Crystal structure of human DOT1L in complex with inhibitor FED2 Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa）	Not recorded	AW0 5'-deoxy-5'-[(3-{[(4-methylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]adenosine × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.15 Å R-free 0.221
4ER0 Crystal Structure of human DOT1L in complex with inhibitor FED1 Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa）	Not recorded	AW1 5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5'-deoxyadenosine × 1 UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, 0.5 mM inhibitor in H2O, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.272
4ER3 Crystal Structure of Human DOT1L in complex with inhibitor EPZ004777 Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–351（351 aa）	Not recorded	0QK 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.6M (NH4)2SO4, 0.01M MgCl2, 0.1M NaCaCo, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.282
4ER5 Crystal structure of human DOT1L in complex with 2 molecules of EPZ004777 Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–412（412 aa）	Not recorded	0QK 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 2 UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.57 Å R-free 0.218
4ER6 Crystal structure of human DOT1L in complex with inhibitor SGC0946 Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–412（412 aa）	Not recorded	BR BROMIDE ION × 1 AW2 5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.230
4ER7 Crystal Structure of human DOT1L in complex with inhibitor SGC0947 Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa）	Not recorded	AW3 5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.242
4HRA Crystal Structure of DOT1L in Complex with EPZ-5676 Deposited 2012-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–416（416 aa） Fragment：UNP residues 1-416	Not recorded	EP6 5'-[{cis-3-[2-(5-tert-butyl-1H-benzimidazol-2-yl)ethyl]cyclobutyl}(propan-2-yl)amino]-5'-deoxyadenosine × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 MM SODIUM ACETATE, 1.8-2.0 M AMMONIUM SULFATE, 5 MM TCEP, SOAKING THE COMPOUND INTO CROSS-LINKED DOT1L-SAM CRYSTAL, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.256
4WVL Structure-Guided DOT1L Probe Optimization by Label-Free Ligand Displacement Deposited 2014-11-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–347（347 aa）	Not recorded	3US N-[4-(acetylamino)butyl]-5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5'-deoxyadenosine × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；293 K；A 5-fold excess of 50 mM 5-iodotubercidin (in DMSO) was mixed with protein and crystallized by using the hanging-drop vapor diffusion method at 20 degree in conditions containing 1.8 M (NH4)2SO4, 0.1 M NaAc-pH4.9. Crystals were transferred into stabilization buffer (2.5 M (NH4)2SO4, 0.1 M NaAc-pH4.9, 0.5 M NaCl), incubated with 100 uM inhibitor.	Resolution 2.41 Å R-free 0.197
5DRT Crystal structure of Dot1L in complex with inhibitor CPD2 [2-(2-(5-((2-chlorophenoxy)methyl)-1H-tetrazol-1-yl)acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide] Deposited 2015-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–333（332 aa） Fragment：UNP residues 2-333	Not recorded	5EG 2-({5-[(2-chlorophenoxy)methyl]-1H-tetrazol-1-yl}acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M K/Na tartrate 0.1M Hepes pH7.2	Resolution 2.69 Å R-free 0.197
5DRT Crystal structure of Dot1L in complex with inhibitor CPD2 [2-(2-(5-((2-chlorophenoxy)methyl)-1H-tetrazol-1-yl)acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide] Deposited 2015-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–333（332 aa） Fragment：UNP residues 2-333	Not recorded	5EG 2-({5-[(2-chlorophenoxy)methyl]-1H-tetrazol-1-yl}acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M K/Na tartrate 0.1M Hepes pH7.2	Resolution 2.69 Å R-free 0.197
5DRY Crystal structure of Dot1L in complex with inhibitor CPD3 [N-(1-(2-chlorophenyl)-1H-indol-6-yl)-2-(2-(5-(2-chlorophenyl)-1H-tetrazol-1-yl)acetyl)hydrazinecarboxamide] Deposited 2015-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–333（332 aa） Fragment：UNP residues 2-333	Not recorded	K POTASSIUM ION × 1 5EK N-[1-(2-chlorophenyl)-1H-indol-6-yl]-2-{[5-(2-chlorophenyl)-1H-tetrazol-1-yl]acetyl}hydrazinecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.2M K/Na tartrate 0.1M Hepes pH7.2	Resolution 2.41 Å R-free 0.199
5DRY Crystal structure of Dot1L in complex with inhibitor CPD3 [N-(1-(2-chlorophenyl)-1H-indol-6-yl)-2-(2-(5-(2-chlorophenyl)-1H-tetrazol-1-yl)acetyl)hydrazinecarboxamide] Deposited 2015-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–333（332 aa） Fragment：UNP residues 2-333	Not recorded	K POTASSIUM ION × 1 5EK N-[1-(2-chlorophenyl)-1H-indol-6-yl]-2-{[5-(2-chlorophenyl)-1H-tetrazol-1-yl]acetyl}hydrazinecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.2M K/Na tartrate 0.1M Hepes pH7.2	Resolution 2.41 Å R-free 0.199
5DSX Crystal structure of Dot1L in complex with inhibitor CPD10 [6'-chloro-1,4-dimethyl-5'-(2-methyl-6-((4-(methylamino)pyrimidin-2-yl)amino)-1H-indol-1-yl)-[3,3'-bipyridin]-2(1H)-one] Deposited 2015-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa） Fragment：UNP residues 2-332	Not recorded	K POTASSIUM ION × 1 5EW 6'-chloro-1,4-dimethyl-5'-(2-methyl-6-{[4-(methylamino)pyrimidin-2-yl]amino}-1H-indol-1-yl)-3,3'-bipyridin-2(1H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M K/Na tartrate tetrahydrate, 0.1M Hepes pH6.8	Resolution 2.41 Å R-free 0.202
5DSX Crystal structure of Dot1L in complex with inhibitor CPD10 [6'-chloro-1,4-dimethyl-5'-(2-methyl-6-((4-(methylamino)pyrimidin-2-yl)amino)-1H-indol-1-yl)-[3,3'-bipyridin]-2(1H)-one] Deposited 2015-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa） Fragment：UNP residues 2-332	Not recorded	K POTASSIUM ION × 1 5EW 6'-chloro-1,4-dimethyl-5'-(2-methyl-6-{[4-(methylamino)pyrimidin-2-yl]amino}-1H-indol-1-yl)-3,3'-bipyridin-2(1H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M K/Na tartrate tetrahydrate, 0.1M Hepes pH6.8	Resolution 2.41 Å R-free 0.202
5DT2 Crystal structure of Dot1L in complex with inhibitor CPD11 [N4-methyl-N2-(2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl)pyrimidine-2,4-diamine] Deposited 2015-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa） Fragment：UNP residues 2-332	Not recorded	5EV N~4~-methyl-N~2~-[2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl]pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M lithium sulfate 0.1M sodium citrate tribasic dihydrate 0.3M ammonium sulfate	Resolution 2.30 Å R-free 0.213
5DT2 Crystal structure of Dot1L in complex with inhibitor CPD11 [N4-methyl-N2-(2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl)pyrimidine-2,4-diamine] Deposited 2015-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa） Fragment：UNP residues 2-332	Not recorded	5EV N~4~-methyl-N~2~-[2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl]pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M lithium sulfate 0.1M sodium citrate tribasic dihydrate 0.3M ammonium sulfate	Resolution 2.30 Å R-free 0.213
5DTQ Crystal structure of Dot1L in complex with inhibitor CPD3 [(2,6-dichlorophenyl)(quinolin-6-yl)methanone] Deposited 2015-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	5F6 (2,6-dichlorophenyl)(quinolin-6-yl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.6M K/Na tartrate, 0.1M Hepes pH6.6	Resolution 2.61 Å R-free 0.208
5DTQ Crystal structure of Dot1L in complex with inhibitor CPD3 [(2,6-dichlorophenyl)(quinolin-6-yl)methanone] Deposited 2015-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	5F6 (2,6-dichlorophenyl)(quinolin-6-yl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.6M K/Na tartrate, 0.1M Hepes pH6.6	Resolution 2.61 Å R-free 0.208
5DTR Crystal structure of Dot1L in complex with inhibitor CPD5 [N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine] Deposited 2015-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	5F7 N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.2M K/Na tartrate, 0.1M Hepes pH6.6	Resolution 2.34 Å R-free 0.210
5DTR Crystal structure of Dot1L in complex with inhibitor CPD5 [N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine] Deposited 2015-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	5F7 N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.2M K/Na tartrate, 0.1M Hepes pH6.6	Resolution 2.34 Å R-free 0.210
5JUW complex of Dot1l with SS148 Deposited 2016-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa） Fragment：UNP residues 1-420	Not recorded	UNX UNKNOWN LIGAND × 22 6NR (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.5 M ammonium sulfate, 0.1 M ammonium acetate	Resolution 2.28 Å R-free 0.215
5MVS Crystal structure of Dot1L in complex with adenosine and inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine] Deposited 2017-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–332（331 aa） Chain B 2–332（331 aa）	Not recorded	ADN ADENOSINE × 2 5JJ N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine × 2 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M K/Na tartrate, 0.1M Hepes pH6.8	Resolution 2.18 Å R-free 0.187
5MW3 Crystal structure of Dot1L in complex with inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine] and inhibitor CPD2 [(R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine] Deposited 2017-01-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	5JJ N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine × 1 5JT (3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M K/Na tartrate, 0.1M Hepes pH6.6	Resolution 2.09 Å R-free 0.193
5MW3 Crystal structure of Dot1L in complex with inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine] and inhibitor CPD2 [(R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine] Deposited 2017-01-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	5JJ N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine × 1 5JT (3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.4M K/Na tartrate, 0.1M Hepes pH6.6	Resolution 2.09 Å R-free 0.193
5MW4 Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide] Deposited 2017-01-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	5JU N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.92M Lithium sulfate monohydrate, 0.1M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate	Resolution 2.19 Å R-free 0.202
5MW4 Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide] Deposited 2017-01-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	5JU N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.92M Lithium sulfate monohydrate, 0.1M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate	Resolution 2.19 Å R-free 0.202
6IN3 Crystal structure of DOT1L in complex with 18-Crown-6 Deposited 2018-10-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–330（327 aa）	Not recorded	O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M ammonium sulfate, 22 mM acetic acid, 78 mM sodium acetate	Resolution 2.30 Å R-free 0.213
6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22	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: dodecameric	Chain K 1–416（416 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07	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 X 5–332（328 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07	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: dodecameric	Chain X 5–332（328 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.80 Å
6JN2 Crystal structure of the coiled-coil domains of human DOT1L in complex with AF10 Deposited 2019-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 470–550（81 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；289 K；0.1 M SODIUM ACETATE PH 4.8, 0.3 M KSCN, 8% V/V PENTAERYTHRITOL ETHOXYLATE (3/4 EO/OH),	Resolution 3.60 Å R-free 0.381
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain K 2–416（415 aa） Chain M 2–416（415 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.	Resolution 2.96 Å
6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14	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: dodecameric	Chain K 3–416（414 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16	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: dodecameric	Chain K 2–416（415 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing	Resolution 3.90 Å
6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19	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: dodecameric	Chain K 2–416（415 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.	Resolution 3.54 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13	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: dodecameric	Chain K 2–332（331 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging	Resolution 3.50 Å
6TE6 Crystal structure of Dot1L in complex with an inhibitor (compound 3). Deposited 2019-11-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	N4W ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.28 M Na/K-tartrate 0.1 M Hepes pH 6.6	Resolution 1.98 Å R-free 0.201
6TE6 Crystal structure of Dot1L in complex with an inhibitor (compound 3). Deposited 2019-11-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	N4W ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.28 M Na/K-tartrate 0.1 M Hepes pH 6.6	Resolution 1.98 Å R-free 0.201
6TEL Crystal structure of Dot1L in complex with an inhibitor (compound 10). Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	N4Z ~{N}1-[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]-~{N}2-(4-methoxy-6-piperazin-1-yl-1,3,5-triazin-2-yl)-4-methylsulfonyl-benzene-1,2-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.28 M K/Na tartrate 0.1 M Hepes pH 7.0	Resolution 2.19 Å R-free 0.212
6TEL Crystal structure of Dot1L in complex with an inhibitor (compound 10). Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	N4Z ~{N}1-[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]-~{N}2-(4-methoxy-6-piperazin-1-yl-1,3,5-triazin-2-yl)-4-methylsulfonyl-benzene-1,2-diamine × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.28 M K/Na tartrate 0.1 M Hepes pH 7.0	Resolution 2.19 Å R-free 0.212
6TEN Crystal structure of Dot1L in complex with an inhibitor (compound 11). Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–332（331 aa）	Not recorded	N5K 3-[(4-azanyl-6-methoxy-1,3,5-triazin-2-yl)amino]-4-[[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]amino]benzenesulfonamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.5 M Li sulfate 0.1 M Hepes pH 7.0	Resolution 2.21 Å R-free 0.201
6TEN Crystal structure of Dot1L in complex with an inhibitor (compound 11). Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–332（331 aa）	Not recorded	N5K 3-[(4-azanyl-6-methoxy-1,3,5-triazin-2-yl)amino]-4-[[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]amino]benzenesulfonamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.5 M Li sulfate 0.1 M Hepes pH 7.0	Resolution 2.21 Å R-free 0.201
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain K 1–416（416 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.32 Å
7EDP Crystal structure of AF10-DOT1L complex Deposited 2021-03-16	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 610–649（40 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% Ethylene glycol	Resolution 2.20 Å R-free 0.268
7S7E STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PEPTIDE Deposited 2021-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 998–1006（9 aa） Fragment：DOT1L(998-1006) PEPTIDE	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE	Resolution 2.04 Å R-free 0.235
7S7F STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PHOSPHOPEPTIDE Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 998–1006（9 aa） Fragment：DOT1L(998-1006) PHOSPHOPEPTIDE	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE	Resolution 1.88 Å R-free 0.217
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25	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: dodecameric	Chain K 5–332（328 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain K 5–332（328 aa） Chain M 5–332（328 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å

47 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DOT1L_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–333； UniProt 2–332 Author chain B； PDBConstruct 3–333； UniProt 2–332

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5dtm
Deposition date deposition_date	2015-09-18
Structure title title	Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide]
Keywords keywords	Inhibitor, Complex, Methyltransferase, transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.64 Å
Radius of gyration Rg (electron density) rg_electron	27.75 Å
Forward intensity I(0) i0	85403800.00
Molecular weight molecular_weight	73144.0 kDa
Excluded volume excluded_volume	91661 Å³
Envelope volume envelope_volume	113960 Å³
Hydration-shell volume shell_volume	34320 Å³
Envelope diameter envelope_diameter	107.2 Å
Shell Rg shell_rg	34.65 Å
Envelope Rg envelope_rg	28.10 Å
Shape Rg shape_rg	27.73 Å
Total Rg total_rg	28.51 Å
Total atoms total_atoms	5163
Residues n_residues	638
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	101.4 Å
Rg (real space) rg_real	28.63 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	8.5400e+07
I(0) uncertainty (real space) i0_real_error	1.1770e+06
Rg (reciprocal space) rg_reciprocal	28.64 Å
I(0) (reciprocal space) i0_reciprocal	85400000.0000
Solution quality estimate total_estimate	0.8571
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.379
Kurtosis Kurtosis kurtosis	-0.174
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26520000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-79 specific
Molecular weight formula_weight	38456.6 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5626

GPGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide
Molecular weight formula_weight	297.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	463

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5dtma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.31 — Catalytic, N-terminal domain of histone methyltransferase Dot1l

Domain ID domain_id	d5dtmb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.31 — Catalytic, N-terminal domain of histone methyltransferase Dot1l

CATH v4.4 (4 domains)

Domain ID domain_id	5dtmA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	5dtmA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5dtmB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	5dtmB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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8. Citations (1)

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Unit-cell length a length_a	158.559 Å
Unit-cell length b length_b	158.559 Å
Unit-cell length c length_c	73.396 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	44.000 Å
R factor r_factor	0.1757
R_work r_work	0.1744
R_free r_free	0.1991

fit	/app/data/saxs_computation/dt/5dtm/5dtm.fit
pddf	/app/data/pr_computation/dt/5dtm/5dtm.pr.out
profile	/app/data/saxs_computation/dt/5dtm/5dtm.dat