UniProt Q9NRG4
N-lysine methyltransferase SMYD2 (Q9NRG4)
N-lysine methyltransferase SMYD2 (UniProt Q9NRG4), EC 2.1.1.-, 2.1.1.43: 44 experimental structures and 1 predicted model on GenesisL1, 14 ligands bound, 41 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- Q9NRG4
- Protein
- N-lysine methyltransferase SMYD2
- EC
- 2.1.1.-, 2.1.1.43
- Experimental structures
- 44
- Predicted models
- 1
- Ligands
- 14
- Pockets
- 41 · 7 records with a druggable one
Structures
45 records of Q9NRG4 in the MolNFT archive: 44 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3RIB | Human lysine methyltransferase Smyd2 in complex with AdoHcy | x-ray diffraction | A, B | — | — |
| 3RIB | Human lysine methyltransferase SMYD2 in complex with adohcy | x-ray diffraction | A, B | — | — |
| 3S7B | Structural Basis of Substrate Methylation and Inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7B | Structural basis of substrate methylation and inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7D | Structural Basis of Substrate Methylation and Inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7D | Structural basis of substrate methylation and inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7F | Structural Basis of Substrate Methylation and Inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7F | Structural basis of substrate methylation and inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7J | Structural Basis of Substrate Methylation and Inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3S7J | Structural basis of substrate methylation and inhibition of SMYD2 | x-ray diffraction | A | — | — |
| 3TG4 | Structure of SMYD2 in complex with SAM | x-ray diffraction | A | — | — |
| 3TG4 | Structure of SMYD2 in complex with SAM | x-ray diffraction | A | — | — |
| 3TG5 | Structure of SMYD2 in complex with p53 and SAH | x-ray diffraction | A | — | — |
| 3TG5 | Structure of SMYD2 in complex with P53 and sah | x-ray diffraction | A | — | — |
| 4O6F | Structural Basis of Estrogen Receptor Alpha Methylation Mediated by Histone Methyltransferase SmyD2 | x-ray diffraction | A | — | — |
| 4O6F | Structural basis of estrogen receptor alpha methylation mediated by histone methyltransferase SMYD2 | x-ray diffraction | A | — | — |
| 4WUY | Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active… | x-ray diffraction | A | — | — |
| 4WUY | Crystal structure of protein lysine methyltransferase SMYD2 in complex with lly-507, a cell-active… | x-ray diffraction | A | — | — |
| 4YND | The Discovery of A-893, A New Cell-Active Benzoxazi Inhibitor of Lysine Methyltransferase SMYD2 | x-ray diffraction | A | — | — |
| 4YND | The discovery of a-893, a new cell-active benzoxazinone inhibitor of lysine methyltransferase SMYD2 | x-ray diffraction | A | — | — |
| 5ARF | SMYD2 in complex with small molecule inhibitor compound-2 | x-ray diffraction | A | — | — |
| 5ARF | SMYD2 in complex with small molecule inhibitor compound-2 | x-ray diffraction | A | — | — |
| 5ARG | SMYD2 in complex with SGC probe BAY-598 | x-ray diffraction | A | — | — |
| 5ARG | SMYD2 in complex with sgc probe bay-598 | x-ray diffraction | A | — | — |
| 5KJK | SMYD2 in complex with AZ370 | x-ray diffraction | A | SAM, 6T1, ZN | 3 (best 0.77) |
| 5KJK | SMYD2 in complex with AZ370 | x-ray diffraction | A | 6T1, ZN | — |
| 5KJL | SMYD2 in complex with AZ378 | x-ray diffraction | A | ZN | — |
| 5KJL | SMYD2 in complex with AZ378 | x-ray diffraction | A | ZN | — |
| 5KJM | SMYD2 in complex with AZ931 | x-ray diffraction | A | 6TM, ZN | — |
| 5KJM | SMYD2 in complex with AZ931 | x-ray diffraction | A | 6TM, ZN | — |
| 5KJN | SMYD2 in complex with AZ506 | x-ray diffraction | A | SAM, NA, 6TL, ZN | 6 (best 0.77) |
| 5KJN | SMYD2 in complex with AZ506 | x-ray diffraction | A | NA, 6TL, ZN | — |
| 5V3H | Crystal structure of SMYD2 with SAM and EPZ033294 | x-ray diffraction | A | ZN, 8WG | — |
| 5V3H | Crystal structure of SMYD2 with SAM and EPZ033294 | x-ray diffraction | A | ZN, 8WG | — |
| 5WCG | SET and MYND Domain Containing protein 2 | x-ray diffraction | A | ZN, A4M, UNX | 5 (best 0.78) |
| 5WCG | Set and mynd domain containing protein 2 | x-ray diffraction | A | ZN, A4M, UNX | — |
| 6CBX | Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497 | x-ray diffraction | A, B | ZN, EW1, CL, UNX | 9 (best 0.79) |
| 6CBX | Crystal structure of human set and mynd domain containing protein 2 with MTF1497 | x-ray diffraction | A, B | ZN, EW1, CL, UNX | — |
| 6CBY | Crystal structure of human SET and MYND Domain Containing protein 2 with MTF9975 | x-ray diffraction | A, B | ZN, EW4 | — |
| 6CBY | Crystal structure of human set and mynd domain containing protein 2 with MTF9975 | x-ray diffraction | A, B | ZN, EW4 | — |
| 6MON | Crystal structure of human SMYD2 in complex with Nle-peptide inhibitor | x-ray diffraction | A, B | ZN, SAH | 12 (best 0.81) |
| 6MON | Crystal structure of human SMYD2 in complex with nle-peptide inhibitor | x-ray diffraction | A, B | ZN | — |
| 6N3G | Crystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene glycol | x-ray diffraction | A | SAH, NI, ZN | 3 (best 0.80) |
| 6N3G | Crystal structure of histone lysine methyltransferase SMYD2 in complex with polyethylene glycol | x-ray diffraction | A | NI, ZN | — |
| Q9NRG4 | AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q9NRG4) | predicted | A | — | 3 (best 0.78) |
Ligands
- ZN · Zinc ion · in 20 records
- UNX · Unknown atom or ion · in 4 records
- 6T1 · 2-[2-[1-[2-(3,4-dichlorophenyl)ethyl]azetidin-3-yl]oxyphenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-4-carboxamide · in 2 records
- 6TL · 5-[2-[4-[2-(1~{H}-indol-3-yl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-3-carboxamide · in 2 records
- 6TM · 6-[2-[4-[2-(3,4-dichlorophenyl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)-2~{H}-pyrazolo[3,4-b]pyridine-4-carboxamide · in 2 records
- 8WG · N-[1-({1-[(4-chlorophenyl)methyl]-1H-pyrazol-4-yl}methyl)azetidin-3-yl]-1-cyclopropyl-1H-1,2,3-triazole-4-carboxamide · in 2 records
- A4M · [3-(6-amino-2-methyl-9H-purin-9-yl)azetidin-1-yl]{5-[(4-cycloheptylpiperazin-1-yl)methyl]-1-methyl-1H-pyrazol-3-yl}methanone · in 2 records
- CL · Chloride ion · in 2 records
- EW1 · [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl) azetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl)-1H-pyrrol-3-yl]methanone · in 2 records
- EW4 · [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)-3-methylazetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl)-1H-pyrrol-3-yl]methanone · in 2 records
- NA · Sodium ion · in 2 records
- NI · Nickel (II) ion · in 2 records
- SAH · S-adenosyl-L-homocysteine · in 2 records
- SAM · S-adenosylmethionine · in 2 records
Experiment against prediction
- 6MON chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.21 Å
- 6MON chain B against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.22 Å
- 5KJK chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.24 Å
- 6N3G chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.39 Å
- 3S7F chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.20 Å
- 3S7F chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.20 Å
- 3S7B chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.21 Å
- 3S7B chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.21 Å
- 6MON chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.21 Å
- 5KJK chain A against the predicted model Q9NRG4: TM-score 1.00, RMSD 0.24 Å
Elsewhere
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