Menin
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1–459 Chain A； UniProt 537–593 | 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 |
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 9C4X | 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 |
| 8VA5 Menin mutant - T349M in complex with Ziftomenib (KO-539) Deposited 2023-12-11 | 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：T349M 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 |
| 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 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 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：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 |
| 9C4Y Menin mutant - T349M 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：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 |
