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8vpq

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML

Method: ELECTRON MICROSCOPY Dmax: 144.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Kelch repeat and BTB domain-containing protein 4

Homo sapiens

UniProt Q9NVX7

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–534 Chain B； UniProt 1–534 Not recorded Histone deacetylase 1 × 1 （Q13547） REST corepressor 1 × 1 （Q9UKL0） ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 Å

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 8VPQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2EQX Solution structure of the BACK domain of Kelch repeat and BTB domain-containing protein 4 Deposited 2007-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 142–239（98 aa） Fragment：BACK domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.15mM 13C-15N PROTEIN; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
8VOJ The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6 Deposited 2024-01-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–534（534 aa）
Chain B 1–534（534 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.77 Å
8VRT The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant Deposited 2024-01-22 Different construct Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–534（518 aa）
Chain B 17–534（518 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
9DTG The cryo-EM structure of apo KBTBD4 Deposited 2024-09-30 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 1–534（534 aa）
Chain B 1–534（534 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
9DTQ The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant Deposited 2024-10-01 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 17–534（518 aa）
Chain E 17–534（518 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9GGL Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171 Deposited 2024-08-13 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 17–534（518 aa）
Chain C 17–534（518 aa）
Not recorded ZN ZINC ION × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9GGM Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–534（518 aa）
Chain C 17–534（518 aa）
Mutation：Indel mutation R313PRR Mutation：Indel mutation R313PRR ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
9GGN Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171 Deposited 2024-08-13 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–534（518 aa）
Chain C 17–534（518 aa）
Not recorded A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9I2C Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171 Deposited 2025-01-20 Different construct Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–534（518 aa）
Chain C 17–534（518 aa）
Not recorded A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KBTB4_HUMAN
Isoform Q9NVX7-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–536； UniProt 1–534 Author chain B； PDBConstruct 1–536； UniProt 1–534

Histone deacetylase 1

Homo sapiens

UniProt Q13547

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–482 Not recorded Isoform 2 of Kelch repeat and BTB domain-containing protein 4 × 2 （Q9NVX7） REST corepressor 1 × 1 （Q9UKL0） ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 Å

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 8VPQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4BKX The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex Deposited 2013-04-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–482（482 aa）
Not recorded ZN ZINC ION × 2 ACT ACETATE ION × 2 K POTASSIUM ION × 4 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400
Resolution 3.00 Å R-free 0.261
5ICN HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4 Deposited 2016-02-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–376（376 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400
Resolution 3.30 Å R-free 0.299
6Z2J The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–482（482 aa）
Chain E 1–482（482 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 3 sec, blot force 10.
Resolution 4.00 Å
6Z2K The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–482（482 aa）
Chain E 1–482（482 aa）
Chain I 1–482（482 aa）
Chain K 1–482（482 aa）
Not recorded ZN ZINC ION × 4 K POTASSIUM ION × 8 IHP INOSITOL HEXAKISPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 3 sec, blot force 10.
Resolution 4.50 Å
7AO8 Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex Deposited 2020-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–482（482 aa）
Chain E 1–482（482 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10
Resolution 4.50 Å
7AO9 Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex Deposited 2020-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–482（482 aa）
Chain E 1–482（482 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10
Resolution 6.10 Å
7AOA Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex Deposited 2020-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–482（482 aa）
Chain E 1–482（482 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10
Resolution 19.40 Å
7SME p107 pocket domain complexed with HDAC1 peptide Deposited 2021-10-25 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 413–422（10 aa） Fragment：UNP residues 413-422
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate
Resolution 2.64 Å R-free 0.277
8VOJ The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6 Deposited 2024-01-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–482（482 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.77 Å
8VRT The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant Deposited 2024-01-22 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–482（482 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
9R4I An auto inhibitory loop in the MiDAC histone deacetylase complex Deposited 2025-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–482（482 aa）
Chain D 1–482（482 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES, 25 mM KCl, 1 micromolar Inositol Hexaphosphate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HDAC1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–482； UniProt 1–482

REST corepressor 1

Homo sapiens

UniProt Q9UKL0

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 1–485 Not recorded Isoform 2 of Kelch repeat and BTB domain-containing protein 4 × 2 （Q9NVX7） Histone deacetylase 1 × 1 （Q13547） ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 Å

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 8VPQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2IW5 Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase Deposited 2006-06-26 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 286–482（197 aa） Fragment：FRAGMENT OF SANT1, LINKER REGION AND SANT2 DOMAIN, RESIDUES 286-482
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 NH4 AMMONIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL.
Resolution 2.57 Å R-free 0.212
2UXN Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation Deposited 2007-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 286–482（197 aa） Fragment：FRAGMENT OF SANT1, LINKER REGION AND SANT2 DOMAIN, RESIDUES 286-482
Not recorded FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
Resolution 2.72 Å R-free 0.272
2UXX Human LSD1 Histone Demethylase-CoREST in complex with an FAD- tranylcypromine adduct Deposited 2007-03-30 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 286–482（197 aa） Fragment：FRAGMENT OF SANT1, LINKER REGION AND SANT2 DOMAIN, RESIDUES 308-482
Not recorded FAJ FAD-trans-2-Phenylcyclopropylamine Adduct × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL.
Resolution 2.74 Å R-free 0.260
2V1D Structural basis of LSD1-CoREST selectivity in histone H3 recognition Deposited 2007-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa） Fragment：305-482
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.10 Å R-free 0.239
2X0L Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1. Deposited 2009-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–440（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.252
2XAF Crystal structure of LSD1-CoREST in complex with para-bromo-(+)-cis-2- phenylcyclopropyl-1-amine Deposited 2010-03-31 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 TCF 3-(4-BROMOPHENYL)PROPANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SODIUM/POTASSIUM TARTRATE, ADA BUFFER PH 6.5
Resolution 3.25 Å R-free 0.229
2XAG Crystal structure of LSD1-CoREST in complex with para-bromo-(-)-trans- 2-phenylcyclopropyl-1-amine Deposited 2010-03-31 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 TCF 3-(4-BROMOPHENYL)PROPANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
Resolution 3.10 Å R-free 0.245
2XAH Crystal structure of LSD1-CoREST in complex with (+)-trans-2- phenylcyclopropyl-1-amine Deposited 2010-03-31 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 3PL 3-PHENYLPROPANAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
Resolution 3.10 Å R-free 0.228
2XAJ Crystal structure of LSD1-CoREST in complex with (-)-trans-2- phenylcyclopropyl-1-amine Deposited 2010-03-31 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 TCA PHENYLETHYLENECARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
Resolution 3.30 Å R-free 0.227
2XAQ Crystal structure of LSD1-CoREST in complex with a tranylcypromine derivative (MC2584, 13b) Deposited 2010-03-31 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 M84 3-{4-[(PHENYLCARBONYL)AMINO]PHENYL}PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
Resolution 3.20 Å R-free 0.264
2XAS Crystal structure of LSD1-CoREST in complex with a tranylcypromine derivative (MC2580, 14e) Deposited 2010-03-31 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 M80 3-[4-({N-[(BENZYLOXY)CARBONYL]-L-PHENYLALANYL}AMINO)PHENYL]PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
Resolution 3.20 Å R-free 0.220
2Y48 Crystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide Deposited 2011-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa） Fragment：RESIDUES 305-482
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 1.2 M SODIUM/POTASSIUM TARTRATE, 100 MM ADA BUFFER PH 6.5
Resolution 3.00 Å R-free 0.246
3ZMS LSD1-CoREST in complex with INSM1 peptide Deposited 2013-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.96 Å R-free 0.227
3ZMT LSD1-CoREST in complex with PRSFLV peptide Deposited 2013-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 3.10 Å R-free 0.230
3ZMU LSD1-CoREST in complex with PKSFLV peptide Deposited 2013-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 3.20 Å R-free 0.226
3ZMV LSD1-CoREST in complex with PLSFLV peptide Deposited 2013-02-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 3.00 Å R-free 0.258
3ZMZ LSD1-CoREST in complex with PRSFAV peptide Deposited 2013-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 3.00 Å R-free 0.227
3ZN0 LSD1-CoREST in complex with PRSFAA peptide Deposited 2013-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.80 Å R-free 0.244
3ZN1 LSD1-CoREST in complex with PRLYLV peptide Deposited 2013-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 3.10 Å R-free 0.230
4BAY Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST Deposited 2012-09-17 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 308–440（133 aa） Fragment：RESIDUES 308-440
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；20DEG BY HANGING-DROP VAPOR DIFFUSION METHOD BY MIXING EQUAL VOLUMES OF PROTEIN SAMPLES WITH RESERVOIR SOLUTIONS CONTAINING 1.2 M SODIUM/POTASSIUM TARTRATE AND 100 MM N-(2-ACETAMIDO)IMINODIACETIC ACID, PH 6.5
Resolution 3.10 Å R-free 0.226
4UV8 LSD1(KDM1A)-CoREST in complex with 1-Benzyl-Tranylcypromine Deposited 2014-08-05 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 1–482（482 aa）
Not recorded D69 [[(2R,3S,4S)-5-[(4aS,10aS)-4a-[(1S)-3-azanylidene-1,4-diphenyl-butyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-5,10a-dihydro-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentoxy]-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.80 Å R-free 0.237
4UV9 LSD1(KDM1A)-CoREST in complex with 1-Ethyl-Tranylcypromine Deposited 2014-08-05 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 1–482（482 aa）
Not recorded D70 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aS,10aS)-4a-[(1S,3E)-3-imino-1-phenylpentyl]-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PH 6.5
Resolution 3.00 Å R-free 0.246
4UVA LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1R,2S) Deposited 2014-08-05 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 1–482（482 aa）
Not recorded D73 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aS)-4a-[(1S,3E)-3-imino-1-phenylbutyl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PH 6.5
Resolution 2.90 Å R-free 0.232
4UVB LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1S,2R) Deposited 2014-08-05 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 1–482（482 aa）
Not recorded D51 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,7aS)-1-amino-1,10,11-trimethyl-4,6-dioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.80 Å R-free 0.236
4UVC LSD1(KDM1A)-CoREST in complex with 1-Phenyl-Tranylcypromine Deposited 2014-08-05 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 1–482（482 aa）
Not recorded D52 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-[(1S)-1-azanyl-1,3-diphenyl-propyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4aH-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 3.10 Å R-free 0.241
4UXN LSD1(KDM1A)-CoREST in complex with Z-Pro derivative of MC2580 Deposited 2014-08-27 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 M8A benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PH 6.5
Resolution 2.85 Å R-free 0.215
4XBF Structure of LSD1:CoREST in complex with ssRNA Deposited 2014-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain B 308–440（133 aa） Fragment：UNP residues 308-440
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 SO4 SULFATE ION × 20 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT]
Resolution 2.80 Å R-free 0.227
5H6Q Crystal structure of LSD1-CoREST in complex with peptide 11 Deposited 2016-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–440（133 aa） Fragment：UNP RESIDUES 308-440
Not recorded GOL GLYCEROL × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(2-Acetamido) iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate.
Resolution 2.53 Å R-free 0.247
5H6R Crystal structure of LSD1-CoREST in complex with peptide 13 Deposited 2016-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–440（133 aa） Fragment：UNP RESIDUES 308-440
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M N-(2-Acetamido) iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate tetrahydrate
Resolution 2.60 Å R-free 0.231
5L3B Human LSD1/CoREST: LSD1 D556G mutation Deposited 2016-04-06 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Tartrate 1-1.4 M, ADA 100 mM pH 6.5
Resolution 3.30 Å R-free 0.208
5L3C Human LSD1/CoREST: LSD1 E379K mutation Deposited 2016-04-06 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Tartrate 1-1.4 M, ADA 100 mM pH 6.5
Resolution 3.31 Å R-free 0.223
5L3D Human LSD1/CoREST: LSD1 Y761H mutation Deposited 2016-04-06 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Tartrate 1-1.4 M, ADA 100 mM pH 5.6
Resolution 2.60 Å R-free 0.219
5L3E LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor Deposited 2016-04-10 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 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 5 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3 M Na/K Tartrate, 100 mM ADA
Resolution 2.80 Å R-free 0.224
5L3F LSD1-CoREST1 in complex with polymyxin B Deposited 2016-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3 M Na/K Tartrate 100 mM ADA
Resolution 3.50 Å R-free 0.210
5L3G LSD1-CoREST1 in complex with polymyxin E (colistin) Deposited 2016-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3 M Na/K Tartrate 100 mM ADA
Resolution 3.10 Å R-free 0.197
5LBQ LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor Deposited 2016-06-16 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 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 767 N2-(3-(dimethylamino)propyl)-6,7-dimethoxy-N4,N4-dimethylquinazoline-2,4-diamine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM ADA pH 6.5 1.2 M Na/Ka Tartrate
Resolution 3.30 Å R-free 0.250
5LGN Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 19 Deposited 2016-07-07 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 308–440（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6W0 ~{N}-[3-(methoxymethyl)phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；297 K；Sodium Tartrate 1.2 M as precipitant in Sodium Citrate buffer pH 5.6
Resolution 3.20 Å R-free 0.220
5LGT Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 15 Deposited 2016-07-08 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 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6W3 4-methyl-~{N}-[2-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Hanging-drop vapor diffusion method at 20 C by mixing equal volumes of 100 microM LSD1-CoREST solution in 5% (w/v) glycerol, 25 mm potassium phosphate, pH 7.2, with reservoir solutions containing 1.2 M sodium/potassium tartrate and 100 mmN-(2-acetamido)-2-iminodiacetic acid, pH 6.5.
Resolution 3.00 Å R-free 0.230
5LGU Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 34 Deposited 2016-07-08 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 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6W1 4-methyl-~{N}-[2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；The hanging-drop vapor diffusion method at 20 C by mixing equal volumes of 100 microM LSD1-CoREST solution in 5% (w/v) glycerol, 25 mm potassium phosphate, pH 7.2, with reservoir solutions containing 1.2 M sodium/potassium tartrate and 100 mmN-(2-acetamido)-2-iminodiacetic acid, pH 6.5.
Resolution 3.20 Å R-free 0.206
5LHG Structure of the KDM1A/CoREST complex with the inhibitor 4-methyl-N-[4-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide Deposited 2016-07-11 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 4 6X3 4-methyl-N-[4-[[4-[(1-methyl-4-piperidyl)oxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M Na/K tartrate 0.1 M ADA pH 6.0
Resolution 3.34 Å R-free 0.192
5LHH Structure of the KDM1A/CoREST complex with the inhibitor 4-ethyl-N-[3-(methoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide Deposited 2016-07-11 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 6 6X0 4-ethyl-~{N}-[3-(methoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M Na/K tartrate 0.1 M ADA pH 6.0
Resolution 3.05 Å R-free 0.186
5LHI Structure of the KDM1A/CoREST complex with the inhibitor N-[3-(ethoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methylthieno[3,2-b]pyrrole-5-carboxamide Deposited 2016-07-12 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 1–482（482 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6X5 ~{N}-[3-(ethoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M Na/K tartrate 0.1 M ADA pH 6.0
Resolution 3.40 Å R-free 0.225
5X60 Crystal structure of LSD1-CoREST in complex with peptide 9 Deposited 2017-02-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–443（133 aa） Fragment：UNP RESIDUES 311-443
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(2-acetamido)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate.
Resolution 2.69 Å R-free 0.236
5YJB LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile Deposited 2017-10-10 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 311–443（133 aa） Fragment：UNP residues 311-443
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8WC 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (PH 5.5), 1.23M POTASSIUM SODIUM TARTRATE TETRAHYDRATE
Resolution 2.96 Å R-free 0.219
6K3E LSD1/Co-Rest structure with an inhibitor Deposited 2019-05-17 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 311–443（133 aa）
Not recorded CW0 piperidin-4-ylmethyl 4-fluoranyl-4-[[[(1~{R},2~{S})-2-phenylcyclopropyl]amino]methyl]piperidine-1-carboxylate × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ACT ACETATE ION × 2 MLA MALONIC ACID × 3 GOL GLYCEROL × 4 D3U 2-PCPA derivative × 1 EDO 1,2-ETHANEDIOL × 12 PEG DI(HYDROXYETHYL)ETHER × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；36% Tacsimate
Resolution 2.87 Å R-free 0.223
6KGK LSD1-CoREST-S2101 five-membered ring adduct model Deposited 2019-07-12 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 311–443（133 aa）
Not recorded GOL GLYCEROL × 3 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate
Resolution 2.70 Å R-free 0.206
6KGL LSD1-CoREST-S2101 N5 adduct model Deposited 2019-07-12 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 311–443（133 aa）
Not recorded GOL GLYCEROL × 3 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
Resolution 2.70 Å R-free 0.205
6KGM LSD1-CoREST-S2116 five-membered ring adduct model Deposited 2019-07-12 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 311–443（133 aa）
Not recorded GOL GLYCEROL × 5 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
Resolution 2.62 Å R-free 0.195
6KGN LSD1-CoREST-S2116 N5 adduct model Deposited 2019-07-12 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 311–443（133 aa）
Not recorded GOL GLYCEROL × 5 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
Resolution 2.62 Å R-free 0.194
6S35 LSD1/CoREST1 complex with macrocyclic peptide inhibitor Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–485（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；Crystallization: hanging drop, 2 uL total, 1:1 protein-to-reservoir. Protein: 11 mg/mL in 50 mM HEPES, 200 mM NaCl, 2 mM DTT, pH 7.5. Reservoir: 100 mM sodium citrate/citric acid, 1.1 M sodium tartrate, pH 5.5. Soaking: 100 mM sodium citrate/citric acid, 1.5 M sodium tartrate, 10% glycerol, 1 mM ligand, pH 5.5.
Resolution 3.10 Å R-free 0.213
6TE1 Structure of the KDM1A/CoREST complex with the inhibitor 2-[3-{4-chloro-3-[(4-chlorophenyl)ethynyl]phenyl}-1-(3-morpholin-4-ylpropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]-2-oxoethanol Deposited 2019-11-11 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 1–482（482 aa）
Not recorded N4K 5-[4-cyclobutyl-1-[2-(4-piperidin-4-yloxyphenoxy)ethyl]imidazol-2-yl]-4-methyl-thieno[3,2-b]pyrrole × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M NA/K TARTRATE 0.1 M ADA
Resolution 3.11 Å R-free 0.192
6TUY Human LSD1/CoREST bound to the quinazoline inhibitor MC4106 Deposited 2020-01-08 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 1–485（485 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NY8 ~{N}2-[3-(dimethylamino)propyl]-6,7-dimethoxy-~{N}4-[1-(naphthalen-2-ylmethyl)piperidin-4-yl]quinazoline-2,4-diamine × 3 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 5 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20 degrees C in 100 mM N-(2- acetamido)iminodiacetic acid (pH 6.5) and 1.2 M Na-K tartrate
Resolution 2.60 Å R-free 0.223
6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 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 L 289–443（155 aa）
Chain N 289–443（155 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5, 75 mM triammonium citrate, 10% PEG2000-MME, Modified Microbatch under oil
Resolution 4.99 Å R-free 0.277
6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain l 289–443（155 aa）
Chain n 289–443（155 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5, 75 mM triammonium citrate, 10% PEG2000-MME, Modified Microbatch under oil
Resolution 4.99 Å R-free 0.277
6W4K Crystal structure of Lysine Specific Demethylase 1 (LSD1) with CC-90011 Deposited 2020-03-11 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 312–443（132 aa）
Not recorded V0Y 4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxo-1,6-dihydropyrimidin-4-yl]-2-fluorobenzonitrile × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.3M Na Tartrate
Resolution 2.93 Å R-free 0.235
6WC6 Crystal structure of a truncated LSD1:CoREST in the presence of an LSD1-NT peptide Deposited 2020-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–440（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；The LSD1-CoREST complex 10mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 1 mM TCEP) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 5 mM TCEP]. When get crystals, soak the crystals within 5mM LSD1-NT peptide.
Resolution 3.10 Å R-free 0.236
7CDC Crystal structure of LSD1-CoREST in complex with PRSFLVRRP peptide Deposited 2020-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–443（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Resolution 2.64 Å R-free 0.231
7CDD Crystal structure of LSD1-CoREST in complex with PRSFLVRR peptide Deposited 2020-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–443（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Resolution 2.76 Å R-free 0.227
7CDE Crystal structure of LSD1-CoREST in complex with PRSFLVRKR peptide Deposited 2020-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–443（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Resolution 2.68 Å R-free 0.233
7CDF Crystal structure of LSD1-CoREST in complex with PRSFLVRRK peptide Deposited 2020-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–443（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Resolution 2.68 Å R-free 0.241
7CDG Crystal structure of LSD1-CoREST in complex with PRSFLVRRR peptide Deposited 2020-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–443（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Resolution 2.80 Å R-free 0.242
7ZRY Structure of the 2a splicing variant of the full-length human LSD1 bound to CoREST (delta305) Deposited 2022-05-06 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 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.0-1.3 M Na/K Tartrate, 0.1 M ADA pH 6.5
Resolution 2.70 Å R-free 0.241
8BOP LSD1-CoREST in complex with AW4, long soaking Deposited 2022-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 308–443（136 aa）
Not recorded SV9 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)-5-[3-[4-(3-phenylphenyl)phenyl]propanoyl]-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.74 Å R-free 0.262
8BOX LSD1-CoREST in complex with AW4 and SNAG peptide Deposited 2022-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded SV9 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)-5-[3-[4-(3-phenylphenyl)phenyl]propanoyl]-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.82 Å R-free 0.229
8F2Z LSD1-CoREST in complex with AW2, short soaking Deposited 2022-11-09 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 308–443（136 aa）
Not recorded XB3 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-([1,1'-biphenyl]-4-yl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 M Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 3.00 Å R-free 0.246
8F30 LSD1-CoREST in complex with AW2, long soaking Deposited 2022-11-09 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 308–443（136 aa）
Not recorded XB6 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 3.10 Å R-free 0.223
8F59 LSD1-CoREST in complex with AW2 and SNAG peptide Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded XB6 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.80 Å R-free 0.234
8F6S LSD1-CoREST in complex with T105 Deposited 2022-11-17 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 308–443（136 aa）
Not recorded XHT [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 XHX 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.91 Å R-free 0.244
8FDV LSD1-CoREST in complex N-formyl FAD and SNAG peptide Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.95 Å R-free 0.252
8FJ4 LSD1-CoREST in complex with T108, short soaking Deposited 2022-12-19 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 308–443（136 aa）
Not recorded XZU 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-phenylbenzamide × 3 XZQ [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-[3-(phenylcarbamoyl)phenyl]-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.76 Å R-free 0.248
8FJ7 LSD1-CoREST in complex with T108 and SNAG peptide Deposited 2022-12-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded Y0Z [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-2,4-dioxo-5-{3-[3-(phenylcarbamoyl)phenyl]propanoyl}-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.80 Å R-free 0.243
8FQJ LSD1-CoREST in complex with T14, short soaking Deposited 2023-01-06 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 308–443（136 aa）
Not recorded Y66 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4R)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{4-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.90 Å R-free 0.246
8FRI LSD1-CoREST in complex with AW4, short soaking Deposited 2023-01-07 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 308–443（136 aa）
Not recorded Y9K [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-([1~1~,2~1~:2~3~,3~1~-terphenyl]-1~4~-yl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 M Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 2.80 Å R-free 0.241
8FRQ LSD1-CoREST in complex with T14, long soaking Deposited 2023-01-08 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 308–443（136 aa）
Not recorded XF6 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(4aS)-7,8-dimethyl-5-(3-{4-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}propanoyl)-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.89 Å R-free 0.241
8FRV LSD1-CoREST in complex with T17, short soaking Deposited 2023-01-09 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 308–443（136 aa）
Not recorded YAF [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-[3-(dimethylcarbamoyl)phenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.2 Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 2.72 Å R-free 0.248
8FSK LSD1-CoREST in complex with T18, short soaking Deposited 2023-01-10 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 308–443（136 aa）
Not recorded YAO [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 3.13 Å R-free 0.223
8GJ6 LSD1-CoREST in complex with T16 Deposited 2023-03-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 308–443（136 aa）
Not recorded ZSI [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-3-[3-(methylcarbamoyl)phenyl]-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 2.77 Å R-free 0.251
8JF5 Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAS1440 Deposited 2023-05-17 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 311–443（133 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 UEU 4-[5-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-2-[2-fluoranyl-4-(2-methyl-2-oxidanyl-propyl)phenyl]phenyl]-2-fluoranyl-benzenecarbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；100mM ADA pH6.5, 1.22M Na/K Tartrate
Resolution 3.20 Å R-free 0.230
8Q1G LSD1-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2M, ADA 0.1M,
Resolution 2.60 Å R-free 0.255
8Q1H LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail Deposited 2023-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2 M, ADA 0.1M
Resolution 2.90 Å R-free 0.254
8Q1J LSD1 Y391K-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 305–482（178 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartate 1.2 M, ADA 0.1M
Resolution 2.87 Å R-free 0.272
8UL6 LSD1-CoREST in complex with T16, long soaking Deposited 2023-10-16 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 308–443（136 aa）
Not recorded ZSI [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-3-[3-(methylcarbamoyl)phenyl]-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 2.74 Å R-free 0.241
8UL8 LSD1-CoREST in complex with T15, short soaking Deposited 2023-10-16 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 308–443（136 aa）
Not recorded XRK methyl 3-{(1R,3S,3aS,13R)-8-[(2S,3S,4R)-5-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,4,5,6,8-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-3-yl}benzoate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.82 Å R-free 0.247
8ULB LSD1-CoREST in complex with T17, long soaking Deposited 2023-10-16 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 308–443（136 aa）
Not recorded YAF [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-[3-(dimethylcarbamoyl)phenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 3.41 Å R-free 0.216
8ULC LSD1-CoREST in complex with T15, long soaking Deposited 2023-10-16 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 308–443（136 aa）
Not recorded XRK methyl 3-{(1R,3S,3aS,13R)-8-[(2S,3S,4R)-5-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,4,5,6,8-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-3-yl}benzoate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 2.82 Å R-free 0.255
8ULZ LSD1-CoREST in complex with T18 and SNAG peptide Deposited 2023-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded YAO [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 3.32 Å R-free 0.231
8UMQ LSD1-CoREST in complex with T18, long soaking Deposited 2023-10-18 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 308–443（136 aa）
Not recorded YAO [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 3.26 Å R-free 0.209
8UNI LSD1-CoREST with N-formyl-FAD in complex with H3K4M histone tail Deposited 2023-10-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5
Resolution 3.40 Å R-free 0.252
8UOM LSD1-CoREST with N-formyl-FAD in complex with H3dimeK4 histone tail Deposited 2023-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 308–443（136 aa）
Not recorded HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 3.20 Å R-free 0.240
8VOJ The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6 Deposited 2024-01-15 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 86–485（400 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.77 Å
8VRT The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant Deposited 2024-01-22 Different construct Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 86–485（400 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8YM7 Crystal structure of Lysine Specific Demethylase 1 (LSD1) with JH-45 Deposited 2024-03-08 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 310–443（134 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 A1LZJ 4-[5-(4-azanylpiperidin-1-yl)-8-(4-methylphenyl)pyrido[3,4-b]pyrazin-7-yl]-2-fluoranyl-benzenecarbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium acetate pH 4.6 1.2 M Sodium malonate
Resolution 2.83 Å R-free 0.248
9DBP Crystal structure of the LSD1/CoREST histone demethylase in complex with the cofactor FAD and the inhibitor GSK690 Deposited 2024-08-23 Different construct Different mutation/modification 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 312–442（131 aa）
Mutation：K315A,K381A,V425A,R428A FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 A1A5U 4-[2-(4-methylphenyl)-5-{[(3R)-pyrrolidin-3-yl]methoxy}pyridin-3-yl]benzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM ADA, 1.2 - 1.6M N/K and 3% w/v D-(+)-Glucose monohydrate
Resolution 2.66 Å R-free 0.250
9DTQ The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant Deposited 2024-10-01 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 86–485（400 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9DWU CoREST complex bound to U2AF2 Deposited 2024-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 311–379（69 aa） Fragment：UNP residues 311-379
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.14 Å
9EL7 LSD1-CoREST in complex with T105 enantiomer (1R,2S) Deposited 2024-12-04 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 308–443（136 aa）
Not recorded A1BI4 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3S,4R)-5-[(4aS)-7,8-dimethyl-4a-[(1R)-1-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-3-oxopropyl]-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.87 Å R-free 0.242
9EL8 LSD1-CoREST in complex with T105 1S2R enantiomer Deposited 2024-12-04 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 308–443（136 aa）
Not recorded XHT [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 XHX 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.91 Å R-free 0.244
9ELA LSD1-CoREST in complex with T108, long soaking Deposited 2024-12-04 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 308–443（136 aa）
Not recorded XZQ [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-[3-(phenylcarbamoyl)phenyl]-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Resolution 2.85 Å R-free 0.243
9F0A N5 Adduct of LSD1-CoREST in complex with MC4455 Deposited 2024-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 305–482（178 aa）
Not recorded A1H8N [[(2~{S},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{R})-5-[5-[3-[4-[[4-[[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]carbamoyl]pyridin-2-yl]amino]phenyl]propanoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a}~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 M Sodium Tartrate, 0.1 M ADA, pH 6.5
Resolution 3.36 Å R-free 0.234
9FWG LSD1/CoREST bound to bomedemstat Deposited 2024-06-30 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 1–485（485 aa）
Not recorded A1IG2 Bomedemstat FAD adduct × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；100 mM N-(2-Acetamido)iminodiacetic acid (ADA) pH 6.5, 1.2 M Na/K Tartrate. Crystals were soaked in a solution containing 1 mM bomedemstat for 2 hours at 20 degress
Resolution 3.20 Å R-free 0.227
9I2C Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171 Deposited 2025-01-20 Different construct Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 86–248（163 aa）
Not recorded A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

100 other PDB entries and 101 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RCOR1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–485； UniProt 1–485

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 8vpq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vpq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vpq
Deposition date deposition_date2024-01-16
Structure title titleThe structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML
Keywords keywordsprotein degradation, E3 ligase, Neo-substrate, cancer mutation, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.02 Å
Radius of gyration Rg (electron density) rg_electron42.82 Å
Forward intensity I(0) i0446075000.00
Molecular weight molecular_weight171990.0 kDa
Excluded volume excluded_volume214450 ų
Envelope volume envelope_volume298260 ų
Hydration-shell volume shell_volume58556 ų
Envelope diameter envelope_diameter154.1 Å
Shell Rg shell_rg47.20 Å
Envelope Rg envelope_rg42.42 Å
Shape Rg shape_rg42.84 Å
Total Rg total_rg42.96 Å
Total atoms total_atoms12090
Residues n_residues1509
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 dmax144.2 Å
Rg (real space) rg_real43.05 Å
Rg uncertainty (real space) rg_real_error1.37 Å
I(0) (real space) i0_real4.4610e+08
I(0) uncertainty (real space) i0_real_error8.1780e+06
Rg (reciprocal space) rg_reciprocal43.02 Å
I(0) (reciprocal space) i0_reciprocal446100000.0000
Solution quality estimate total_estimate0.8894
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.8 Å
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha63270000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.876
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)