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1nw3

Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase

Method: X-RAY DIFFRACTION Dmax: 88.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

histone methyltransferase DOT1L

Homo sapiens

UniProt Q8TEK3

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 1–416 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

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 1NW3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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
5DTM Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide] Deposited 2015-09-18 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）
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
5DTM Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide] Deposited 2015-09-18 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）
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
5DTQ Crystal structure of Dot1L in complex with inhibitor CPD3 [(2,6-dichlorophenyl)(quinolin-6-yl)methanone] Deposited 2015-09-18 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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 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 2–332（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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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 59 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 1–416； UniProt 1–416

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 1nw3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nw3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nw3
Deposition date deposition_date2003-02-05
Structure title titleStructure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase
Keywords keywordshDot1, histone lysine methyltransferase, TRANSFERASE; TRANSFERASE
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_guinier24.07 Å
Radius of gyration Rg (electron density) rg_electron23.56 Å
Forward intensity I(0) i025570600.00
Molecular weight molecular_weight38506.0 kDa
Excluded volume excluded_volume48106 ų
Envelope volume envelope_volume58956 ų
Hydration-shell volume shell_volume22075 ų
Envelope diameter envelope_diameter90.2 Å
Shell Rg shell_rg29.34 Å
Envelope Rg envelope_rg24.23 Å
Shape Rg shape_rg23.55 Å
Total Rg total_rg24.32 Å
Total atoms total_atoms2712
Residues n_residues328
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 dmax88.5 Å
Rg (real space) rg_real24.27 Å
Rg uncertainty (real space) rg_real_error0.95 Å
I(0) (real space) i0_real2.5570e+07
I(0) uncertainty (real space) i0_real_error3.9300e+05
Rg (reciprocal space) rg_reciprocal24.23 Å
I(0) (reciprocal space) i0_reciprocal25570000.0000
Solution quality estimate total_estimate0.8059
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis0.080
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6392000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.597; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.700; Smooth: 0.982
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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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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1nw3a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.31 — Catalytic, N-terminal domain of histone methyltransferase Dot1l

CATH v4.4 (2 domains)

Domain ID domain_id1nw3A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily60 —
Domain ID domain_id1nw3A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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8. Citations (1)

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9. Files and Curves (10)