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8vha

Crystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate

Method: X-RAY DIFFRACTION Dmax: 128.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isocitrate dehydrogenase [NADP] cytoplasmic

Homo sapiens

UniProt O75874

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–414 Chain B； UniProt 1–414 Mutation：R132Q EE1 (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid × 1 NO3 NITRATE ION × 2 CA CALCIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；277.15 K；160mM NaNO3 and 20% W/V PEG 3350 Resolution 2.28 Å R-free 0.222
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–414 Chain D； UniProt 1–414 Mutation：R132Q EE1 (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid × 1 NO3 NITRATE ION × 1 CA CALCIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；277.15 K；160mM NaNO3 and 20% W/V PEG 3350 Resolution 2.28 Å R-free 0.222

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 8VHA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1T09 Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex NADP Deposited 2004-04-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.270
1T0L Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+) Deposited 2004-04-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG 6000, MES, NADP, isocitrate, calcium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.41 Å R-free 0.253
1T0L Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+) Deposited 2004-04-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG 6000, MES, NADP, isocitrate, calcium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.41 Å R-free 0.253
3INM Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+) Deposited 2009-08-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 CA CALCIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride, 10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt. Precipitant: 100mM MES pH 6.5, 20% PEG 6000. Ratio of protein component to precipitant in initial hanging drop: 2:1., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.262
3INM Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+) Deposited 2009-08-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 CA CALCIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride, 10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt. Precipitant: 100mM MES pH 6.5, 20% PEG 6000. Ratio of protein component to precipitant in initial hanging drop: 2:1., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.262
3MAP Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate Deposited 2010-03-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M Tris-HCl, 2.0M (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.269
3MAR Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP Deposited 2010-03-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；277 K；1.0M Na2HPO4/KH2PO4, pH 8.2, vapor diffusion, hanging drop, temperature 277K
Resolution 3.41 Å R-free 0.289
3MAS Crystal structure of heterodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate Deposited 2010-03-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES-Na, 2% PEG 400, 2.0M (NH4)2SO4, pH 7.5, vapor diffusion, hanging drop, temperature 293K
Resolution 3.20 Å R-free 0.283
4I3K Crystal structure of a metabolic reductase with 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin-2(1H)-one Deposited 2012-11-26 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 SO4 SULFATE ION × 4 1BX 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；10 mM NADPH and 10 mM CaCl2 in a solution of 1.75 M (NH4)2SO4 and 0.1 M NaAc (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.31 Å R-free 0.277
4I3L Crystal structure of a metabolic reductase with 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one Deposited 2012-11-26 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 SO4 SULFATE ION × 2 1BZ 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；10 mM NADPH and 10 mM CaCl2 in a solution of 1.75 M (NH4)2SO4 and 0.1 M NaAc (pH 5.7), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.29 Å R-free 0.293
4KZO Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.20 Å R-free 0.221
4KZO Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.20 Å R-free 0.221
4L03 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.10 Å R-free 0.230
4L03 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CA CALCIUM ION × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.10 Å R-free 0.230
4L04 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded AKG 2-OXOGLUTARIC ACID × 2 CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.87 Å R-free 0.259
4L04 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Not recorded AKG 2-OXOGLUTARIC ACID × 2 CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.87 Å R-free 0.259
4L04 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–414（414 aa）
Chain F 1–414（414 aa）
Not recorded AKG 2-OXOGLUTARIC ACID × 2 CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.87 Å R-free 0.259
4L06 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：Y139D Mutation：Y139D CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.28 Å R-free 0.270
4L06 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：Y139D Mutation：Y139D CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.28 Å R-free 0.270
4L06 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate Deposited 2013-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–414（414 aa）
Chain F 1–414（414 aa）
Mutation：Y139D Mutation：Y139D CA CALCIUM ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；298 K；16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K
Resolution 2.28 Å R-free 0.270
4UMX IDH1 R132H in complex with cpd 1 Deposited 2014-05-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H VVS 2,6-bis(1H-imidazol-1-ylmethyl)-4-(2,4,4-trimethylpentan-2-yl)phenol × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PEG 8K 26%, TRIS 100MM PH 8, MALONATE NA 200MM
Resolution 1.88 Å R-free 0.211
4UMY IDH1 R132H in complex with cpd 1 Deposited 2014-05-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：YES Mutation：YES SO4 SULFATE ION × 4 GOL GLYCEROL × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PEG 5000 MME 22% - BIS-TRIS 100MM PH 6.5 - AMMONIUM SULFATE 220 MM
Resolution 2.07 Å R-free 0.224
4XRX Crystal structure of a metabolic reductase with (E)-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one Deposited 2015-01-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 42V 5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.6；293 K；10 mM NADPH and 10 mM CaCl2 in a solution of 1.75 M (NH4)2SO4 and 0.1 M NaAc (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.277
4XS3 Crystal structure of a metabolic reductase with (E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one Deposited 2015-01-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H 42W (E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.6；293 K；10 mM NADPH and 10 mM CaCl2 in a solution of 1.75 M (NH4)2SO4 and 0.1 M NaAc (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.29 Å R-free 0.283
5DE1 Crystal structure of human IDH1 in complex with GSK321A Deposited 2015-08-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–414（413 aa）
Chain B 2–414（413 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 59D (7R)-1-(4-fluorobenzyl)-N-{3-[(1S)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrol-2-ylcarbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；18-23% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-Tris, pH 7.0, 10mM NADP+
Resolution 2.25 Å R-free 0.258
5K10 Cryo-EM structure of isocitrate dehydrogenase (IDH1) Deposited 2016-05-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–413（411 aa）
Chain B 3–413（411 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (LEICA EM GP)
Resolution 3.80 Å
5K11 Cryo-EM structure of isocitrate dehydrogenase (IDH1) in inhibitor-bound state Deposited 2016-05-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–413（411 aa）
Chain B 3–413（411 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (LEICA EM GP)
Resolution 3.80 Å
5L57 Crystal structure of Iso-citrate Dehydrogenase R132H in complex with a novel inhibitor (compound 13a) Deposited 2016-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 6N3 (1~{R},5~{S})-3-[6-(3-methylbutoxy)-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]-3-azabicyclo[3.1.0]hexane-6-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.12M Ethylene Glycols, 0.1M Bicine pH 8.5, 50% (40% v/v PEG 500 MME, 20% w/v PEG 20K) [Morpheus A9] 200 plus 200nl drops (Mosquito)
Resolution 2.69 Å R-free 0.256
5L58 Crystal structure of Iso-citrate Dehydrogenase 1 [IDH1 (R132H)] in complex with a novel inhibitor (Compound 2) Deposited 2016-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 6MX 2-[(3~{R})-1-[6-cyclohexylsulfanyl-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]pyrrolidin-3-yl]ethanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；200nl of protein with 200nl of a reservoir solution of 0.06M Divalents, 0.1M Tris / Bicine pH 8.5, 50% (40% v/v PEG 500 MME, 20% w/v PEG 20K) [Morpheus E9]
Resolution 3.04 Å R-free 0.264
5LGE Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor related to BAY 1436032 Deposited 2016-07-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 1 6VN 2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；PROTEIN BUFFER: 15 MG/ML. PROTEIN IN 25 MM HEPES, 300 MM NACL, 5 MM BETA-ME, COMPLETE PROTEASE INHIBITOR MIXTURE, PH 7.7 RESERVOIR: 100 MM BIS-TRIS, PH 7.0, 200 MM CA-ACETATE, 20.0 %(W/V) PEG 3350
Resolution 2.70 Å R-free 0.230
5LGE Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor related to BAY 1436032 Deposited 2016-07-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 6VN 2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；PROTEIN BUFFER: 15 MG/ML. PROTEIN IN 25 MM HEPES, 300 MM NACL, 5 MM BETA-ME, COMPLETE PROTEASE INHIBITOR MIXTURE, PH 7.7 RESERVOIR: 100 MM BIS-TRIS, PH 7.0, 200 MM CA-ACETATE, 20.0 %(W/V) PEG 3350
Resolution 2.70 Å R-free 0.230
5SUN IDH1 R132H in complex with IDH146 Deposited 2016-08-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 70Q 3-benzyl-N-[3-(dimethylsulfamoyl)phenyl]-4-oxo-3,4-dihydrophthalazine-1-carboxamide × 2 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；27% PEG3350, 0.22M lithium sulfate
Resolution 2.48 Å R-free 0.221
5SVF IDH1 R132H in complex with IDH125 Deposited 2016-08-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain C 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 70P (4S)-3-(2-{[(1S)-1-phenylethyl]amino}pyrimidin-4-yl)-4-(propan-2-yl)-1,3-oxazolidin-2-one × 2 FLC CITRATE ANION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris pH6.5, 1.45M tri-sodium citrate dihydrate
Resolution 2.34 Å R-free 0.223
5SVF IDH1 R132H in complex with IDH125 Deposited 2016-08-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 70P (4S)-3-(2-{[(1S)-1-phenylethyl]amino}pyrimidin-4-yl)-4-(propan-2-yl)-1,3-oxazolidin-2-one × 2 FLC CITRATE ANION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris pH6.5, 1.45M tri-sodium citrate dihydrate
Resolution 2.34 Å R-free 0.223
5TQH IDH1 R132H mutant in complex with IDH889 Deposited 2016-10-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain C 1–414（414 aa）
Mutation：R132H Mutation：R132H FLC CITRATE ANION × 2 7J2 (4S)-3-[2-({(1S)-1-[5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl]ethyl}amino)pyrimidin-4-yl]-4-(propan-2-yl)-1,3-oxazolidin-2-one × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；co-crystallization with protein concentration at 10mG/mL and compound at 250uM; reservoir solution contains 1.6M tri-ammonium citrate and 0.1M Bis-Tris (pH5.5)
Resolution 2.20 Å R-free 0.225
5TQH IDH1 R132H mutant in complex with IDH889 Deposited 2016-10-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132H Mutation：R132H FLC CITRATE ANION × 2 7J2 (4S)-3-[2-({(1S)-1-[5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl]ethyl}amino)pyrimidin-4-yl]-4-(propan-2-yl)-1,3-oxazolidin-2-one × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；co-crystallization with protein concentration at 10mG/mL and compound at 250uM; reservoir solution contains 1.6M tri-ammonium citrate and 0.1M Bis-Tris (pH5.5)
Resolution 2.20 Å R-free 0.225
5YFM Human isocitrate dehydrogenase 1 bound with NADP Deposited 2017-09-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 20% PEG 8000
Resolution 2.40 Å R-free 0.239
5YFM Human isocitrate dehydrogenase 1 bound with NADP Deposited 2017-09-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 20% PEG 8000
Resolution 2.40 Å R-free 0.239
5YFN Human isocitrate dehydrogenase 1 bound with isocitrate Deposited 2017-09-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M HEPES sodium pH7.5, 0.8 M sodium phosphate, 0.8 M potassium phosphate
Resolution 2.50 Å R-free 0.226
6ADG Crystal Structures of IDH1 R132H in complex with AG-881 Deposited 2018-08-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MG MAGNESIUM ION × 2 9UO 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 25%(w/v) Polyethylene glycol 3,350, 0.1M Cesium chloride
Resolution 3.00 Å R-free 0.244
6ADG Crystal Structures of IDH1 R132H in complex with AG-881 Deposited 2018-08-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Mutation：R132H 9UO 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 25%(w/v) Polyethylene glycol 3,350, 0.1M Cesium chloride
Resolution 3.00 Å R-free 0.244
6B0Z IDH1 R132H mutant in complex with IDH305 Deposited 2017-09-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain C 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 C81 (4R)-4-[(1S)-1-fluoroethyl]-3-[2-({(1S)-1-[4-methyl-2'-(trifluoromethyl)[3,4'-bipyridin]-6-yl]ethyl}amino)pyrimidin-4-yl]-1,3-oxazolidin-2-one × 3 FLC CITRATE ANION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；co-crystallization of protein (20-24mG/mL) /compound complex at 1/1.5 molar ratio; reservoir solution: 1.5-1.8M Tri Ammonium Citrate, 0.1M Bis-Tris pH6.5
Resolution 2.33 Å R-free 0.235
6B0Z IDH1 R132H mutant in complex with IDH305 Deposited 2017-09-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132H Mutation：R132H NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 C81 (4R)-4-[(1S)-1-fluoroethyl]-3-[2-({(1S)-1-[4-methyl-2'-(trifluoromethyl)[3,4'-bipyridin]-6-yl]ethyl}amino)pyrimidin-4-yl]-1,3-oxazolidin-2-one × 3 FLC CITRATE ANION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；co-crystallization of protein (20-24mG/mL) /compound complex at 1/1.5 molar ratio; reservoir solution: 1.5-1.8M Tri Ammonium Citrate, 0.1M Bis-Tris pH6.5
Resolution 2.33 Å R-free 0.235
6BKX Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd1 Deposited 2017-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 ICT ISOCITRIC ACID × 2 DWP (6aS,7S,9R,10aS)-7,10a-dimethyl-8-oxo-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；290 K；20% PEG 3350, 0.2M Potassium/Sodium tartrate
Resolution 1.65 Å R-free 0.187
6BKX Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd1 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 ICT ISOCITRIC ACID × 2 DWP (6aS,7S,9R,10aS)-7,10a-dimethyl-8-oxo-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；290 K；20% PEG 3350, 0.2M Potassium/Sodium tartrate
Resolution 1.65 Å R-free 0.187
6BKY Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Not recorded LMR (2S)-2-hydroxybutanedioic acid × 1 MG MAGNESIUM ION × 2 K32 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；290 K；20% PEG3350, 0.15M D,L-Malic acid pH 7.0
Resolution 2.17 Å R-free 0.221
6BKY Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–414（414 aa）
Chain F 1–414（414 aa）
Not recorded LMR (2S)-2-hydroxybutanedioic acid × 1 MG MAGNESIUM ION × 1 K32 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；290 K；20% PEG3350, 0.15M D,L-Malic acid pH 7.0
Resolution 2.17 Å R-free 0.221
6BKY Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded LMR (2S)-2-hydroxybutanedioic acid × 1 MG MAGNESIUM ION × 1 K32 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；290 K；20% PEG3350, 0.15M D,L-Malic acid pH 7.0
Resolution 2.17 Å R-free 0.221
6BKZ Novel Modes of Inhibition of Wild-Type IDH1: Non-equivalent Allosteric Inhibition with Cmpd3 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 DWM (7R)-1-[(4-fluorophenyl)methyl]-N-{3-[(1R)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrole-2-carbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；18% PEG8K, 0.2M Calcium Acetate, 0.1M Na Cacodylate pH6.5
Resolution 2.01 Å R-free 0.204
6BL0 Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of His315 with Cmpd11 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 DWJ (5aS,6S,8S,9aS)-2-(benzenecarbonyl)-6-methyl-7-oxo-9a-phenyl-4,5,5a,6,7,8,9,9a-octahydro-2H-benzo[g]indazole-8-carbonitrile × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；20% PEG 1500, 0.2M Sodium Chloride, 5% Ethylene Glycol, 0.1M HEPES pH 7.5
Resolution 2.17 Å R-free 0.227
6BL0 Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of His315 with Cmpd11 Deposited 2017-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；20% PEG 1500, 0.2M Sodium Chloride, 5% Ethylene Glycol, 0.1M HEPES pH 7.5
Resolution 2.17 Å R-free 0.227
6BL1 Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd13 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded ICT ISOCITRIC ACID × 2 DWG (6aS,7S,9S,10aS)-7-methyl-8-oxo-10a-phenyl-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；290 K；2% PEG3350, 0.2M Potassium/Sodium tartrate
Resolution 2.02 Å R-free 0.223
6BL1 Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd13 Deposited 2017-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded ICT ISOCITRIC ACID × 2 DWG (6aS,7S,9S,10aS)-7-methyl-8-oxo-10a-phenyl-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；290 K；2% PEG3350, 0.2M Potassium/Sodium tartrate
Resolution 2.02 Å R-free 0.223
6BL2 Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd15 Deposited 2017-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain C 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 ICT ISOCITRIC ACID × 2 DWS 3-[(6aS,7S,9S,10aS)-9-cyano-7-methyl-8-oxo-2-(phenylamino)-6,6a,7,8,9,10-hexahydrobenzo[h]quinazolin-10a(5H)-yl]benzoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；15% PEG3350, 0.1M Succinic acid pH 7.0
Resolution 1.92 Å R-free 0.211
6BL2 Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd15 Deposited 2017-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–414（414 aa）
Not recorded CA CALCIUM ION × 2 ICT ISOCITRIC ACID × 2 DWS 3-[(6aS,7S,9S,10aS)-9-cyano-7-methyl-8-oxo-2-(phenylamino)-6,6a,7,8,9,10-hexahydrobenzo[h]quinazolin-10a(5H)-yl]benzoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；15% PEG3350, 0.1M Succinic acid pH 7.0
Resolution 1.92 Å R-free 0.211
6IO0 Human IDH1 R132C mutant complexed with compound A. Deposited 2018-10-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132C Mutation：R132C AOU (2E)-3-{3-[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazole-4-carbonyl]-1-methyl-1H-indol-7-yl}prop-2-enoic acid × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CIT CITRIC ACID × 3 GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.5M ammonium citrate tribasic (pH 7.0), 2.5mM DTT. micro-seeding.
Resolution 2.20 Å R-free 0.255
6O2Y Crystal structure of IDH1 R132H mutant in complex with compound 24 Deposited 2019-02-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H LJY 4-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methoxybenzonitrile × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG MME 5000, 0.1 M Bicine pH 8.5, and 0.2 M Sodium formate.
Resolution 2.80 Å R-free 0.275
6O2Y Crystal structure of IDH1 R132H mutant in complex with compound 24 Deposited 2019-02-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Mutation：R132H LJY 4-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methoxybenzonitrile × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG MME 5000, 0.1 M Bicine pH 8.5, and 0.2 M Sodium formate.
Resolution 2.80 Å R-free 0.275
6O2Z Crystal structure of IDH1 R132H mutant in complex with compound 32 Deposited 2019-02-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H LJV 6-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methylpyridine-3-carbonitrile × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.8 M Tri-ammonium citrate pH 6.5
Resolution 2.50 Å R-free 0.234
6PAY Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity Deposited 2019-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain D 1–414（414 aa）
Not recorded ICT ISOCITRIC ACID × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；20% PEG3350, 10% Tacsimate, pH 5.0
Resolution 2.20 Å R-free 0.242
6PAY Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity Deposited 2019-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Not recorded ICT ISOCITRIC ACID × 2 MG MAGNESIUM ION × 2 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；20% PEG3350, 10% Tacsimate, pH 5.0
Resolution 2.20 Å R-free 0.242
6Q6F Crystal structure of IDH1 R132H in complex with HMS101 Deposited 2018-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H HJQ (2~{R})-2-[2-[(3~{R})-3-(4-fluorophenyl)pyrrolidin-1-yl]ethyl]-1,4-dimethyl-piperazine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M di-ammonium citrate, 20% PEG 3350
Resolution 3.30 Å R-free 0.288
6U4J Crystal structure of IDH1 R132H mutant in complex with FT-2102 Deposited 2019-08-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CL CHLORIDE ION × 2 PWV 5-{[(1S)-1-(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)ethyl]amino}-1-methyl-6-oxo-1,6-dihydropyridine-2-carbonitrile × 2 FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3000, 0.1 M Sodium citrate
Resolution 2.11 Å R-free 0.220
6VEI Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with NADPH and AG-881 (Vorasidenib) Inhibitor Deposited 2020-01-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 SO4 SULFATE ION × 1 33O 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol × 1 PEG DI(HYDROXYETHYL)ETHER × 4 ACT ACETATE ION × 1 MLA MALONIC ACID × 1 9UO 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine × 1 MLT D-MALATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；20% PEG 3350, 8% Tacsimate pH 4.0
Resolution 2.10 Å R-free 0.195
6VG0 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC ISOCITRATE DEHYDROGENASE (IDH1) R132H MUTANT IN COMPLEX WITH NADPH and AGI-15056 Deposited 2020-01-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 QWM N~2~,N~4~-bis[(1R)-1-cyclopropylethyl]-6-[6-(trifluoromethyl)pyridin-2-yl]-1,3,5-triazine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.25 M ammonium sulfate, 0.1M sodium citrate pH 5.6, 23% PEG 4000
Resolution 2.66 Å R-free 0.264
6VG0 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC ISOCITRATE DEHYDROGENASE (IDH1) R132H MUTANT IN COMPLEX WITH NADPH and AGI-15056 Deposited 2020-01-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 QWM N~2~,N~4~-bis[(1R)-1-cyclopropylethyl]-6-[6-(trifluoromethyl)pyridin-2-yl]-1,3,5-triazine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.25 M ammonium sulfate, 0.1M sodium citrate pH 5.6, 23% PEG 4000
Resolution 2.66 Å R-free 0.264
7PJM Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and Ca2+/2-Oxoglutarate Deposited 2021-08-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132C, S280F Mutation：R132C, S280F AKG 2-OXOGLUTARIC ACID × 2 GOL GLYCEROL × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；15-20 % PEG 3350, Calcium acetate hydrate, BISTRIS
Resolution 2.10 Å R-free 0.210
7PJM Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and Ca2+/2-Oxoglutarate Deposited 2021-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Mutation：R132C, S280F AKG 2-OXOGLUTARIC ACID × 2 GOL GLYCEROL × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；15-20 % PEG 3350, Calcium acetate hydrate, BISTRIS
Resolution 2.10 Å R-free 0.210
7PJN Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and inhibitor DS-1001B Deposited 2021-08-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132C, S280F Mutation：R132C, S280F 7SU (E)-3-(1-(5-(2-fluoropropan-2-yl)-3-(2,4,6-trichlorophenyl)isoxazole-4-carbonyl)-3-methyl-1H-indol-4-yl)acrylic acid × 2 CIT CITRIC ACID × 3 GOL GLYCEROL × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2 M Ammonium citrate tribasic, DTT 2 mM
Resolution 2.45 Å R-free 0.228
7PJN Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and inhibitor DS-1001B Deposited 2021-08-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R132C, S280F 7SU (E)-3-(1-(5-(2-fluoropropan-2-yl)-3-(2,4,6-trichlorophenyl)isoxazole-4-carbonyl)-3-methyl-1H-indol-4-yl)acrylic acid × 2 CIT CITRIC ACID × 2 GOL GLYCEROL × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2 M Ammonium citrate tribasic, DTT 2 mM
Resolution 2.45 Å R-free 0.228
8BAY Crystal Structure of IDH1 variant R132C S280F in complex with NADPH, Ca2+ and 3-butyl-2-oxoglutarate Deposited 2022-10-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132C, S280F Mutation：R132C, S280F GOL GLYCEROL × 3 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 QDC (R)-3-butyl-2-oxopentanedioic acid × 2 QD8 (S)-3-butyl-2-oxopentanedioic acid × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；15-20 % PEG 3350, Calcium acetate hydrate, BISTRIS
Resolution 2.35 Å R-free 0.223
8BAY Crystal Structure of IDH1 variant R132C S280F in complex with NADPH, Ca2+ and 3-butyl-2-oxoglutarate Deposited 2022-10-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Mutation：R132C, S280F GOL GLYCEROL × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 QDC (R)-3-butyl-2-oxopentanedioic acid × 2 QD8 (S)-3-butyl-2-oxopentanedioic acid × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；15-20 % PEG 3350, Calcium acetate hydrate, BISTRIS
Resolution 2.35 Å R-free 0.223
8HB9 Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053 Deposited 2022-10-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain AAA 1–414（414 aa）
Chain DDD 1–414（414 aa）
Not recorded R1R [2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；315 K；24% PEG 3350, 8% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.243
8HB9 Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053 Deposited 2022-10-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain AAA 1–414（414 aa）
Chain DDD 1–414（414 aa）
Not recorded R1R [2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；315 K；24% PEG 3350, 8% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.243
8HB9 Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053 Deposited 2022-10-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain BBB 1–414（414 aa）
Chain CCC 1–414（414 aa）
Not recorded R1R [2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；315 K；24% PEG 3350, 8% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.243
8T7D Crystal structure of wild type IDH1 bound to compound 1 Deposited 2023-06-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded ZT3 N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium Cacodylate, pH6.5, 0.2M NaCl, 2M Ammonium Sulfate
Resolution 3.44 Å R-free 0.267
8T7D Crystal structure of wild type IDH1 bound to compound 1 Deposited 2023-06-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Not recorded ZT3 N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium Cacodylate, pH6.5, 0.2M NaCl, 2M Ammonium Sulfate
Resolution 3.44 Å R-free 0.267
8T7N Crystal structure of the R132H mutant of IDH1 bound to compound 1 Deposited 2023-06-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ZT3 N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG3350, 0.45 M Di-Ammonium Tartrate
Resolution 2.26 Å R-free 0.254
8T7O Crystal structure of the R132H mutant of IDH1 bound to AG-120 Deposited 2023-06-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 IV3 ivosidenib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG3350, 0.45 M Di-Ammonium Tartrate
Resolution 2.05 Å R-free 0.255
8VH9 Crystal Structure of Human IDH1 R132Q in complex with NADPH Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132Q Mutation：R132Q GOL GLYCEROL × 5 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；200 mM ammonium citrate tribasic pH 7.0 and 26% (w/v) PEG 3350
Resolution 2.13 Å R-free 0.215
8VHB Crystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132Q Mutation：R132Q AKG 2-OXOGLUTARIC ACID × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 5 SCN THIOCYANATE ION × 10 CL CHLORIDE ION × 2 CA CALCIUM ION × 2 EE1 (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277.15 K；200mM NaSCN and 21%(w/v) PEG 3350
Resolution 1.89 Å R-free 0.206
8VHB Crystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132Q Mutation：R132Q AKG 2-OXOGLUTARIC ACID × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 3 SCN THIOCYANATE ION × 5 CL CHLORIDE ION × 2 CA CALCIUM ION × 2 EE1 (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277.15 K；200mM NaSCN and 21%(w/v) PEG 3350
Resolution 1.89 Å R-free 0.206
8VHC Crystal Structure of Human IDH1 R132Q in complex with NADPH Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132Q Mutation：R132Q GOL GLYCEROL × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；100mM Bis-Tris, 220mM Ammonium Sulfate, and 20%(w/v) PEG 3350
Resolution 2.44 Å R-free 0.240
8VHD Crystal Structure of Human IDH1 R132Q in complex with NADPH and Isocitrate Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132Q Mutation：R132Q NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 IOD IODIDE ION × 2 CA CALCIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；100mM Bis-tris propane, 200mM Sodium Iodide, 24%(w/v) PEG 3350
Resolution 2.38 Å R-free 0.220
8VHD Crystal Structure of Human IDH1 R132Q in complex with NADPH and Isocitrate Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132Q Mutation：R132Q NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 IOD IODIDE ION × 2 CA CALCIUM ION × 2 GOL GLYCEROL × 3 ICT ISOCITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；100mM Bis-tris propane, 200mM Sodium Iodide, 24%(w/v) PEG 3350
Resolution 2.38 Å R-free 0.220
8VHE Crystal Structure of Human IDH1 R132Q in Complex with NADPH-TCEP Adduct Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132Q Mutation：R132Q A1AAX 3,3',3''-({(4R)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1,4-dihydropyridin-4-yl}-lambda~5~-phosphanetriyl)tripropanoic acid × 2 GOL GLYCEROL × 6 CL CHLORIDE ION × 2 CA CALCIUM ION × 2 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277.15 K；200 mM KSCN, 24% (w/v) PEG 6000, and 5 mM TCEP
Resolution 2.16 Å R-free 0.223
8VHE Crystal Structure of Human IDH1 R132Q in Complex with NADPH-TCEP Adduct Deposited 2023-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Mutation：R132Q Mutation：R132Q A1AAX 3,3',3''-({(4R)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1,4-dihydropyridin-4-yl}-lambda~5~-phosphanetriyl)tripropanoic acid × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 2 CA CALCIUM ION × 2 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277.15 K；200 mM KSCN, 24% (w/v) PEG 6000, and 5 mM TCEP
Resolution 2.16 Å R-free 0.223
9B81 Crystal structure of wild type IDH1 bound to compound 4 Deposited 2024-03-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded A1AI4 2-methyl-2-(6-{4-[(2S)-1,1,1-trifluoro-2-hydroxypropan-2-yl]benzoyl}-6,11-dihydro-5H-pyrido[2,3-b][1,5]benzodiazepin-8-yl)propanenitrile × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium Cacodylate, pH6.5, 0.2M NaCl, 2M Ammonium Sulfate
Resolution 2.56 Å R-free 0.233
9M82 Crystal Structure of Human IDH1 in Complex with Kinsenoside Deposited 2025-03-11 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Not recorded A1EOQ Kinsenoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289.15 K；0.5 M Ammonium Sulfate; 0.1 M Mes, pH6.0 15% PEG4000
Resolution 3.08 Å R-free 0.301
9YHA Cryo-EM structure of IDH1 R132H Deposited 2025-09-30 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H Mutation：R132H NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9YHB Cryo-EM structure of IDH1 R132H C269S Deposited 2025-09-30 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Mutation：R132H, C269S Mutation：R132H, C269S NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å

59 other PDB entries and 91 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IDHC_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 17–430； UniProt 1–414 Author chain B； PDBConstruct 17–430； UniProt 1–414 Author chain C； PDBConstruct 17–430； UniProt 1–414 Author chain D； PDBConstruct 17–430； UniProt 1–414

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 8vha

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8vha
Deposition date deposition_date2023-12-31
Structure title titleCrystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate
Keywords keywordsOXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier39.71 Å
Radius of gyration Rg (electron density) rg_electron39.23 Å
Forward intensity I(0) i0541908000.00
Molecular weight molecular_weight189180.0 kDa
Excluded volume excluded_volume235900 ų
Envelope volume envelope_volume302990 ų
Hydration-shell volume shell_volume62348 ų
Envelope diameter envelope_diameter133.6 Å
Shell Rg shell_rg46.80 Å
Envelope Rg envelope_rg38.72 Å
Shape Rg shape_rg39.25 Å
Total Rg total_rg39.52 Å
Total atoms total_atoms13387
Residues n_residues1649
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 dmax128.1 Å
Rg (real space) rg_real39.61 Å
Rg uncertainty (real space) rg_real_error1.33 Å
I(0) (real space) i0_real5.4190e+08
I(0) uncertainty (real space) i0_real_error9.9710e+06
Rg (reciprocal space) rg_reciprocal39.68 Å
I(0) (reciprocal space) i0_reciprocal541900000.0000
Solution quality estimate total_estimate0.8980
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.6 Å
Skewness Skewness skewness0.227
Kurtosis Kurtosis kurtosis-0.586
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha155300000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.913
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)