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8va5

Menin mutant - T349M in complex with Ziftomenib (KO-539)

Method: X-RAY DIFFRACTION Dmax: 84.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Menin

Homo sapiens

UniProt O00255

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–459 Chain A； UniProt 537–593 Mutation：T349M K5O Ziftomenib × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350 Resolution 1.30 Å R-free 0.186

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 8VA5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3U84 Crystal Structure of Human Menin Deposited 2011-10-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.4 M sodium acetate, pH 6.5, vapor diffusion, sitting drop, temperature 277K
Resolution 2.50 Å R-free 0.235
3U84 Crystal Structure of Human Menin Deposited 2011-10-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–459（458 aa）
Chain B 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.4 M sodium acetate, pH 6.5, vapor diffusion, sitting drop, temperature 277K
Resolution 2.50 Å R-free 0.235
3U84 Crystal Structure of Human Menin Deposited 2011-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Chain B 2–459（458 aa）
Chain B 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.4 M sodium acetate, pH 6.5, vapor diffusion, sitting drop, temperature 277K
Resolution 2.50 Å R-free 0.235
3U85 Crystal structure of human menin in complex with MLL1 Deposited 2011-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.00 Å R-free 0.258
3U85 Crystal structure of human menin in complex with MLL1 Deposited 2011-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.00 Å R-free 0.258
3U86 Crystal structure of human menin in complex with JunD Deposited 2011-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 2.84 Å R-free 0.245
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 4 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–459（458 aa）
Chain B 520–610（91 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 1 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
4GPQ Structural insights into inhibition of the bivalent menin-MLL interaction by small molecules in leukemia Deposited 2012-08-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Mutation：A541t PEG DI(HYDROXYETHYL)ETHER × 2 PG4 TETRAETHYLENE GLYCOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP
Resolution 1.46 Å R-free 0.176
4GQ3 Human menin with bound inhibitor MI-2 Deposited 2012-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Mutation：A541t 0RO 4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-propylthieno[2,3-d]pyrimidine × 1 PEG DI(HYDROXYETHYL)ETHER × 1 UNX UNKNOWN LIGAND × 5 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 200 mM 0RO, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.56 Å R-free 0.214
4GQ4 Human menin with bound inhibitor MI-2-2 Deposited 2012-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Mutation：a541t 0RT 4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine × 1 UNX UNKNOWN LIGAND × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 4 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), NBm1 peptide, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 200 mM 0RT, VAPOR DIFFUSION, SITTING DROP
Resolution 1.27 Å R-free 0.182
4GQ6 Human menin in complex with MLL peptide Deposited 2012-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–593（593 aa）
Mutation：a541t SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), NBm1 peptide, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 1:1 molar ratio with MBM1 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.55 Å R-free 0.189
4I80 Crystal structure of human menin in complex with a high-affinity macrocyclic peptidomimetics Deposited 2012-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–459（458 aa）
Chain A 520–610（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.10 Å R-free 0.245
4OG3 Human menin with bound inhibitor MIV-3R Deposited 2014-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Not recorded SO4 SULFATE ION × 1 2S6 4-(3-{4-[(R)-cyclopentyl(hydroxy)phenylmethyl]piperidin-1-yl}propoxy)benzonitrile × 1 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 2.01 Å R-free 0.208
4OG4 Human menin with bound inhibitor MIV-3S Deposited 2014-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Not recorded SO4 SULFATE ION × 1 2VK 4-(3-{4-[(S)-cyclopentyl(hydroxy)phenylmethyl]piperidin-1-yl}propoxy)benzonitrile × 1 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 DMS DIMETHYL SULFOXIDE × 4 TBF TERT-BUTYL FORMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.45 Å R-free 0.189
4OG5 Human menin with bound inhibitor MIV-5 Deposited 2014-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Not recorded 2S7 4-(3-{4-[(S)-cyclopentyl(hydroxy)pyridin-2-ylmethyl]piperidin-1-yl}propoxy)benzonitrile × 1 SO4 SULFATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 DMS DIMETHYL SULFOXIDE × 3 TBF TERT-BUTYL FORMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.63 Å R-free 0.194
4OG6 Human menin with bound inhibitor MIV-4 Deposited 2014-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Not recorded SO4 SULFATE ION × 1 2S9 4-(3-{4-[(R)-cyclopentyl(3-fluorophenyl)hydroxymethyl]piperidin-1-yl}propoxy)benzonitrile × 1 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.49 Å R-free 0.188
4OG7 Human menin with bound inhibitor MIV-7 Deposited 2014-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Not recorded SO4 SULFATE ION × 1 2SE 4-(3-{4-[(S)-cyclopentyl(hydroxy)pyridin-2-ylmethyl]piperidin-1-yl}propoxy)benzenesulfonamide × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 2.08 Å R-free 0.222
4OG8 Human menin with bound inhibitor MIV-6R Deposited 2014-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–593（593 aa）
Not recorded TBF TERT-BUTYL FORMATE × 2 2SF 4-(3-{4-[(R)-amino(cyclopentyl)phenylmethyl]piperidin-1-yl}propoxy)benzonitrile × 1 PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 3 DMS DIMETHYL SULFOXIDE × 3 PGA 2-PHOSPHOGLYCOLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.53 Å R-free 0.176
4X5Y Menin in complex with MI-503 Deposited 2014-12-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：unp residues 1-459; unp residues 537-593
Chain A 537–593（57 aa） Fragment：unp residues 1-459; unp residues 537-593
Mutation：A541T Mutation：A541T 3XW 4-methyl-1-(1H-pyrazol-4-ylmethyl)-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 3 PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.59 Å R-free 0.205
4X5Z menin in complex with MI-136 Deposited 2014-12-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：unp residues 1-459; unp residues 537-593
Chain A 537–593（57 aa） Fragment：unp residues 1-459; unp residues 537-593
Mutation：A541T Mutation：A541T SO4 SULFATE ION × 4 3XY 5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 PG4 TETRAETHYLENE GLYCOL × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.86 Å R-free 0.208
5DB0 Menin in complex with MI-352 Deposited 2015-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T PG4 TETRAETHYLENE GLYCOL × 3 SO4 SULFATE ION × 4 DMS DIMETHYL SULFOXIDE × 4 58P 1-[(2S)-2,3-dihydroxypropyl]-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1 H-indole-2-carbonitrile × 1 6E6 1-[(2R)-2,3-dihydroxypropyl]-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.50 Å R-free 0.185
5DB1 Menin in complex with MI-336 Deposited 2015-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-489, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-489, 537-593
Mutation：A541T Mutation：A541T 58O 6-methoxy-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 3 SO4 SULFATE ION × 5 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.86 Å R-free 0.197
5DB2 Menin in complex with MI-389 Deposited 2015-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 58R 2-{2-cyano-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indol-1-yl}aceta mide × 1 DMS DIMETHYL SULFOXIDE × 3 PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 5 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.54 Å R-free 0.188
5DB3 Menin in complex with MI-574 Deposited 2015-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T DMS DIMETHYL SULFOXIDE × 3 PG4 TETRAETHYLENE GLYCOL × 2 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 58Q 6-methoxy-4-methyl-1-(1H-pyrazol-4-ylmethyl)-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.71 Å R-free 0.194
5DD9 Menin in complex with MI-326 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 59K 4-[4-(5-methyl-1,3,4-thiadiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine × 1 DMS DIMETHYL SULFOXIDE × 5 PG4 TETRAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.62 Å R-free 0.195
5DDA Menin in complex with MI-333 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 59M 4-{4-[5-(fluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine × 1 DMS DIMETHYL SULFOXIDE × 4 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.83 Å R-free 0.211
5DDB Menin in complex with MI-319 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 59Q 4-{4-[5-(difluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine × 1 DMS DIMETHYL SULFOXIDE × 5 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.54 Å R-free 0.210
5DDC Menin in complex with MI-2-3 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 542–598（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 59V 6-(2,2,2-trifluoroethyl)-4-{4-[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}thieno[2,3-d]pyrimidine × 1 DMS DIMETHYL SULFOXIDE × 4 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.62 Å R-free 0.194
5DDD menin in complex with MI-836 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Not recorded 59X 4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(2-fluoroethyl)thieno[2,3-d]pyrimidine × 1 SO4 SULFATE ION × 4 DMS DIMETHYL SULFOXIDE × 4 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 2.14 Å R-free 0.248
5DDE Menin in complex with MI-859 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 5A0 6-(2,2-difluoroethyl)-4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]thieno[2,3-d]pyrimidine × 2 SO4 SULFATE ION × 4 DMS DIMETHYL SULFOXIDE × 4 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.78 Å R-free 0.199
5DDF Menin in complex with MI-273 Deposited 2015-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa） Fragment：UNP residues 1-459, 537-593
Chain A 537–593（57 aa） Fragment：UNP residues 1-459, 537-593
Mutation：A541T Mutation：A541T 5A1 4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(pentafluoroethyl)thieno[2,3-d]pyrimidine × 1 DMS DIMETHYL SULFOXIDE × 4 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.66 Å R-free 0.188
6B41 Menin bound to M-525 Deposited 2017-09-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–610（609 aa）
Not recorded CJV methyl {(1S,2R)-2-[(S)-cyano[1-({1-[4-({1-[4-(dimethylamino)butanoyl]azetidin-3-yl}sulfonyl)phenyl]azetidin-3-yl}methyl)piperidin-4-yl](3-fluorophenyl)methyl]cyclopentyl}carbamate × 1 7PR praseodymium triacetate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.96 M NaCl, 89 mM Bis-Tris pH 6.8, 0.178 M MgCl2 and 10.7 mM Pr Acetate
Resolution 2.61 Å R-free 0.252
6BXH Menin in complex with MI-853 Deposited 2017-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 1 SO4 SULFATE ION × 1 EE7 1-{2-[4-(fluoroacetyl)piperazin-1-yl]ethyl}-4-methyl-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 2.44 Å R-free 0.255
6BY8 Menin in complex with MI-1482 Deposited 2017-12-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Chain A 74–386（313 aa）
Chain A 404–464（61 aa）
Chain A 537–593（57 aa）
Not recorded FNV 4-methyl-1-{[(2R)-5-oxomorpholin-2-yl]methyl}-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 4 PG4 TETRAETHYLENE GLYCOL × 2 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283 K；0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Resolution 1.90 Å R-free 0.188
6E1A Menin bound to M-89 Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–610（609 aa）
Not recorded HL7 (1S,2R)-2-[(4S)-2-methyl-4-{1-[(1-{4-[(pyridin-4-yl)sulfonyl]phenyl}azetidin-3-yl)methyl]piperidin-4-yl}-1,2,3,4-tetrahydroisoquinolin-4-yl]cyclopentyl methylcarbamate × 1 7PR praseodymium triacetate × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2.0 M sodium chloride, 90.9 M Bis-Tris pH 6.5, 0.182 M Magnesium chloride, 9 mM Praseodymium Acetate
Resolution 3.10 Å R-free 0.235
6O5I Menin in complex with MI-3454 Deposited 2019-03-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Chain A 74–386（313 aa）
Chain A 399–459（61 aa）
Chain A 537–593（57 aa）
Not recorded LMY ~{N}-[3-[[2-cyano-4-methyl-5-[[4-[[2-(methylamino)-6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]piperidin-1-yl]methyl]indol-1-yl]methyl]-1-bicyclo[1.1.1]pentanyl]methanamide × 1 DMS DIMETHYL SULFOXIDE × 4 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350.
Resolution 1.24 Å R-free 0.164
6PKC Inhibition of Human Menin by VTP-50469 Deposited 2019-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 552–583（32 aa）
Mutation：A5T Mutation：A5T OP4 5-fluoro-2-({4-[7-({trans-4-[(methylsulfonyl)amino]cyclohexyl}methyl)-2,7-diazaspiro[3.5]nonan-2-yl]pyrimidin-5-yl}oxy)-N,N-di(propan-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；14%(w/v) PEG3350 0.2M Potassium thiocyanate 0.1M MES pH=6.0 15%(v/v) Ethylene glycol
Resolution 1.90 Å R-free 0.206
6PKC Inhibition of Human Menin by VTP-50469 Deposited 2019-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 552–583（32 aa）
Mutation：A5T Mutation：A5T OP4 5-fluoro-2-({4-[7-({trans-4-[(methylsulfonyl)amino]cyclohexyl}methyl)-2,7-diazaspiro[3.5]nonan-2-yl]pyrimidin-5-yl}oxy)-N,N-di(propan-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；14%(w/v) PEG3350 0.2M Potassium thiocyanate 0.1M MES pH=6.0 15%(v/v) Ethylene glycol
Resolution 1.90 Å R-free 0.206
6WNH Menin bound to inhibitor M-808 Deposited 2020-04-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–610（609 aa）
Not recorded 7MM methyl [(1S,2R)-2-{(1S)-2-(azetidin-1-yl)-1-(3-fluorophenyl)-1-[1-({1-[4-({1-[4-(piperidin-1-yl)butanoyl]azetidin-3-yl}sulfonyl)phenyl]azetidin-3-yl}methyl)piperidin-4-yl]ethyl}cyclopentyl]carbamate × 1 7PR praseodymium triacetate × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；1.96 M NaCl, 89 mM Bis-Tris pH 6.8, 0.178 M MgCl2 and 10.7 mM Pr Acetate
Resolution 2.10 Å R-free 0.228
7M4T Menin bound to M-1121 Deposited 2021-03-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–459（458 aa）
Chain A 525–615（91 aa）
Not recorded YQV methyl {(1S,2R)-2-[(1S)-2-(azetidin-1-yl)-1-(3-fluorophenyl)-1-{1-[(3-methoxy-1-{4-[(1S,4S)-5-propanoyl-2,5-diazabicyclo[2.2.1]heptane-2-sulfonyl]phenyl}azetidin-3-yl)methyl]piperidin-4-yl}ethyl]cyclopentyl}carbamate × 1 7PR praseodymium triacetate × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；2.0 M NaCl, 90.9 M Bis-Tris pH 6.5, 0.182 M MgCl2, 10 mM Pr Acetate
Resolution 2.74 Å R-free 0.215
7OA9 Crystal structure of Human Menin in complex with Fragment 21 Deposited 2021-04-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–584（584 aa）
Not recorded V6K (~{E})-2-cyano-3-(4-hydroxyphenyl)-~{N}-(2-morpholin-4-ylethyl)prop-2-enamide × 1 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；12% PEG 3350 14% Glycerol
Resolution 2.10 Å R-free 0.235
8GPN Human menin in complex with H3K79Me2 nucleosome Deposited 2022-08-26 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 × 9 PDB declaration: undecameric
Chain K 1–610（610 aa）
Mutation：N-terminal Ser from cleavage of purification tag No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8IG0 Crystal structure of menin in complex with DS-1594b Deposited 2023-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–610（610 aa）
Chain B 1–610（610 aa）
Not recorded 7IX (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol × 2 UNX UNKNOWN LIGAND × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；283 K；0.1 M Na Cacodylate HCl, pH 6.4/ 1.5 M NaOAc/ 20 mM BaCl2. Complex crystal was prepared with soaking method.
Resolution 2.60 Å R-free 0.266
8IG0 Crystal structure of menin in complex with DS-1594b Deposited 2023-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–610（610 aa）
Chain D 1–610（610 aa）
Not recorded 7IX (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol × 2 UNX UNKNOWN LIGAND × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；283 K；0.1 M Na Cacodylate HCl, pH 6.4/ 1.5 M NaOAc/ 20 mM BaCl2. Complex crystal was prepared with soaking method.
Resolution 2.60 Å R-free 0.266
8VA6 Menin in complex with Ziftomenib (KO-539) Deposited 2023-12-11 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Not recorded K5O Ziftomenib × 1 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 3 DMS DIMETHYL SULFOXIDE × 2 PG4 TETRAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.57 Å R-free 0.193
9C4S Menin mutant G331R in complex with MLL peptide Deposited 2024-06-05 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：G331R Mutation：G331R SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.54 Å R-free 0.202
9C4T menin mutant M327I in complex with MLL peptide Deposited 2024-06-05 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：M327I Mutation：M327I SO4 SULFATE ION × 2 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.46 Å R-free 0.184
9C4U Menin mutant T349M in complex with MLL peptide Deposited 2024-06-05 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：T349M Mutation：T349M PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.57 Å R-free 0.197
9C4V Menin mutant G331D in complex with MLL peptide Deposited 2024-06-05 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：G331D Mutation：G331D SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.47 Å R-free 0.188
9C4W Menin mutant - G331R Deposited 2024-06-05 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：G331R Mutation：G331R PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.40 Å R-free 0.181
9C4X Menin mutant - M327I Deposited 2024-06-05 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：M327I Mutation：M327I PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.58 Å R-free 0.194
9C4Y Menin mutant - T349M Deposited 2024-06-05 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：T349M Mutation：T349M EDO 1,2-ETHANEDIOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.31 Å R-free 0.183
9C4Z Menin mutant - G331D Deposited 2024-06-05 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Chain A 537–593（57 aa）
Mutation：G331D Mutation：G331D PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.40 Å R-free 0.190
9C92 Crystal structure of menin in complex with inhibitor compound 15 Deposited 2024-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 552–583（32 aa）
Mutation：A5T Mutation：A5T A1AVE N-ethyl-5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]-N-(propan-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.1M HEPES pH6.9, 0.2M Na Thiocyanate, 1% Tacsimate, 4% Isopropanol
Resolution 1.90 Å R-free 0.244
9C92 Crystal structure of menin in complex with inhibitor compound 15 Deposited 2024-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 552–583（32 aa）
Mutation：A5T Mutation：A5T A1AVE N-ethyl-5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]-N-(propan-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.1M HEPES pH6.9, 0.2M Na Thiocyanate, 1% Tacsimate, 4% Isopropanol
Resolution 1.90 Å R-free 0.244
9C93 Crystal structure of menin in complex with inhibitor compound 26 Deposited 2024-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 552–583（32 aa）
Mutation：A5T Mutation：A5T A1AVF (1R,5R)-2-({5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]phenyl}methyl)-2-azabicyclo[3.1.0]hexan-3-one × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18% PEG 3350, 0.1M HEPES pH6.9, 0.2M K Thiocyanate, 4% Isopropanol, 1% Tacsimate
Resolution 1.85 Å R-free 0.225
9C93 Crystal structure of menin in complex with inhibitor compound 26 Deposited 2024-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 552–583（32 aa）
Mutation：A5T Mutation：A5T A1AVF (1R,5R)-2-({5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]phenyl}methyl)-2-azabicyclo[3.1.0]hexan-3-one × 1 K POTASSIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18% PEG 3350, 0.1M HEPES pH6.9, 0.2M K Thiocyanate, 4% Isopropanol, 1% Tacsimate
Resolution 1.85 Å R-free 0.225
9C94 Crystal structure of menin in complex with inhibitor compound 20 Deposited 2024-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 552–583（32 aa）
Mutation：A5T Mutation：A5T A1AVG {5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]phenyl}[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22% PEG 3350, 0.1M HEPES pH6.9, 0.2M Na Thiocyanate, 4% Isopropanol, 1% Tacsimate
Resolution 1.98 Å R-free 0.212
9C94 Crystal structure of menin in complex with inhibitor compound 20 Deposited 2024-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 552–583（32 aa）
Mutation：A5T Mutation：A5T A1AVG {5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]phenyl}[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22% PEG 3350, 0.1M HEPES pH6.9, 0.2M Na Thiocyanate, 4% Isopropanol, 1% Tacsimate
Resolution 1.98 Å R-free 0.212
9WKU Wild-type Menin complexed with JNJ-75276617 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；22%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1 M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, PH7.8
Resolution 1.90 Å R-free 0.204
9WKU Wild-type Menin complexed with JNJ-75276617 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；22%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1 M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, PH7.8
Resolution 1.90 Å R-free 0.204
9WKV [M322I] Menin complexed with JNJ-75276617 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18%(w/v) PEG3350, 0.2 M POTASIUM THIOCYANATE, 0.1M MES PH=6.2, 20%(v/v) ETHYLENE GLYCOL, PH 6.2
Resolution 1.80 Å R-free 0.198
9WKV [M322I] Menin complexed with JNJ-75276617 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 4 MG MAGNESIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18%(w/v) PEG3350, 0.2 M POTASIUM THIOCYANATE, 0.1M MES PH=6.2, 20%(v/v) ETHYLENE GLYCOL, PH 6.2
Resolution 1.80 Å R-free 0.198
9WKW Wild-type Menin complexed with DS-1594 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded 7IX (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol × 1 EDO 1,2-ETHANEDIOL × 6 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；22%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1 M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Resolution 1.63 Å R-free 0.176
9WKW Wild-type Menin complexed with DS-1594 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded 7IX (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol × 1 EDO 1,2-ETHANEDIOL × 9 NA SODIUM ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；22%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1 M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Resolution 1.63 Å R-free 0.176
9WKX [M322I] Menin complexed with DS-1594 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded 7IX (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；19%(w/v) PEG3350, 0.2 M POTASIUM THIOCYANATE, 0.1 M MES PH=6.3, 20%(v/v) ETHYLENE GLYCOL, PH 6.5
Resolution 2.25 Å R-free 0.239
9WKX [M322I] Menin complexed with DS-1594 Deposited 2025-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded 7IX (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；19%(w/v) PEG3350, 0.2 M POTASIUM THIOCYANATE, 0.1 M MES PH=6.3, 20%(v/v) ETHYLENE GLYCOL, PH 6.5
Resolution 2.25 Å R-free 0.239
9WN9 Wild-type Menin complexed with DSP-5336 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded 2IZ 5-fluoro-2-[(4-{7-[(1S,3S,4R)-5-methylidene-2-azabicyclo[2.2.2]octane-3-carbonyl]-2,7-diazaspiro[3.5]nonan-2-yl}pyrimidin-5-yl)oxy]-N,N-di(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1 M MES PH=6.0, 20%(v/v) ETHYLENE GLYCOL, PH 6.0
Resolution 1.50 Å R-free 0.214
9WN9 Wild-type Menin complexed with DSP-5336 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded 2IZ 5-fluoro-2-[(4-{7-[(1S,3S,4R)-5-methylidene-2-azabicyclo[2.2.2]octane-3-carbonyl]-2,7-diazaspiro[3.5]nonan-2-yl}pyrimidin-5-yl)oxy]-N,N-di(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1 M MES PH=6.0, 20%(v/v) ETHYLENE GLYCOL, PH 6.0
Resolution 1.50 Å R-free 0.214
9WNA [M322I] Menin complexed with DSP-5336 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded 2IZ 5-fluoro-2-[(4-{7-[(1S,3S,4R)-5-methylidene-2-azabicyclo[2.2.2]octane-3-carbonyl]-2,7-diazaspiro[3.5]nonan-2-yl}pyrimidin-5-yl)oxy]-N,N-di(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1M MES PH=6.0, 20%(v/v) ETHYLENE GLYCOL, PH 6.0
Resolution 2.00 Å R-free 0.212
9WNA [M322I] Menin complexed with DSP-5336 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded 2IZ 5-fluoro-2-[(4-{7-[(1S,3S,4R)-5-methylidene-2-azabicyclo[2.2.2]octane-3-carbonyl]-2,7-diazaspiro[3.5]nonan-2-yl}pyrimidin-5-yl)oxy]-N,N-di(propan-2-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1M MES PH=6.0, 20%(v/v) ETHYLENE GLYCOL, PH 6.0
Resolution 2.00 Å R-free 0.212
9WNI Wild-type Menin complexed with KO-539 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded K5O Ziftomenib × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；24%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, PH7.8
Resolution 2.40 Å R-free 0.275
9WNI Wild-type Menin complexed with KO-539 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded K5O Ziftomenib × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；24%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, PH7.8
Resolution 2.40 Å R-free 0.275
9WNJ [M322I] Menin complexed with KO-539 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–457（456 aa）
Chain A 551–583（33 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 K5O Ziftomenib × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；19%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1M MES PH=6.2, 20%(v/v) ETHYLENE GLYCOL, PH 6.2
Resolution 2.00 Å R-free 0.207
9WNJ [M322I] Menin complexed with KO-539 Deposited 2025-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–457（456 aa）
Chain B 551–583（33 aa）
Not recorded K5O Ziftomenib × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；19%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1M MES PH=6.2, 20%(v/v) ETHYLENE GLYCOL, PH 6.2
Resolution 2.00 Å R-free 0.207
9Z4X MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib) Deposited 2025-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–610（609 aa）
Not recorded BME BETA-MERCAPTOETHANOL × 1 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM Tris pH 6.75 , 5 M NaCl , 0.2 M MgCl2
Resolution 2.95 Å R-free 0.297
9Z4X MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib) Deposited 2025-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–610（609 aa）
Not recorded BME BETA-MERCAPTOETHANOL × 1 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 NA SODIUM ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM Tris pH 6.75 , 5 M NaCl , 0.2 M MgCl2
Resolution 2.95 Å R-free 0.297
9Z4X MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib) Deposited 2025-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–610（609 aa）
Not recorded 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM Tris pH 6.75 , 5 M NaCl , 0.2 M MgCl2
Resolution 2.95 Å R-free 0.297
9Z4X MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib) Deposited 2025-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 2–610（609 aa）
Not recorded 9N6 N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM Tris pH 6.75 , 5 M NaCl , 0.2 M MgCl2
Resolution 2.95 Å R-free 0.297

60 other PDB entries and 80 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEN1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–432； UniProt 1–459 Author chain A； PDBConstruct 433–489； UniProt 537–593

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 8va5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8va5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8va5
Deposition date deposition_date2023-12-11
Structure title titleMenin mutant - T349M in complex with Ziftomenib (KO-539)
Keywords keywordsPROTEIN BINDING; PROTEIN BINDING
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_guinier25.33 Å
Radius of gyration Rg (electron density) rg_electron24.58 Å
Forward intensity I(0) i044647700.00
Molecular weight molecular_weight53360.0 kDa
Excluded volume excluded_volume67425 ų
Envelope volume envelope_volume80265 ų
Hydration-shell volume shell_volume27400 ų
Envelope diameter envelope_diameter89.6 Å
Shell Rg shell_rg31.78 Å
Envelope Rg envelope_rg25.11 Å
Shape Rg shape_rg24.71 Å
Total Rg total_rg24.96 Å
Total atoms total_atoms7508
Residues n_residues466
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 dmax84.1 Å
Rg (real space) rg_real25.37 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real4.4650e+07
I(0) uncertainty (real space) i0_real_error6.1580e+05
Rg (reciprocal space) rg_reciprocal25.36 Å
I(0) (reciprocal space) i0_reciprocal44650000.0000
Solution quality estimate total_estimate0.8807
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1 Å
Skewness Skewness skewness0.429
Kurtosis Kurtosis kurtosis-0.260
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13890000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)