UniProt Q9H7B4
Histone-lysine N-methyltransferase SMYD3 (Q9H7B4)
Histone-lysine N-methyltransferase SMYD3 (UniProt Q9H7B4), EC 2.1.1.354: 41 experimental structures and 1 predicted model on GenesisL1, 17 ligands bound, 10 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- Q9H7B4
- Protein
- Histone-lysine N-methyltransferase SMYD3
- EC
- 2.1.1.354
- Experimental structures
- 41
- Predicted models
- 1
- Ligands
- 17
- Pockets
- 10 · 3 records with a druggable one
Structures
42 records of Q9H7B4 in the MolNFT archive: 41 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3MEK | Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with… | x-ray diffraction | A | — | — |
| 3MEK | Crystal structure of human histone-lysine N-methyltransferase SMYD3 in complex with… | x-ray diffraction | A | — | — |
| 3OXF | Human lysine methyltransferase Smyd3 in complex with AdoHcy (Form I) | x-ray diffraction | A, B | — | — |
| 3OXF | Human lysine methyltransferase SMYD3 in complex with adohcy (form I) | x-ray diffraction | A, B | — | — |
| 3OXG | human lysine methyltransferase Smyd3 in complex with AdoHcy (Form III) | x-ray diffraction | A | — | — |
| 3OXG | Human lysine methyltransferase SMYD3 in complex with adohcy (form III) | x-ray diffraction | A | — | — |
| 3OXL | Human lysine methyltransferase Smyd3 in complex with AdoHcy (Form II) | x-ray diffraction | A | — | — |
| 3OXL | Human lysine methyltransferase SMYD3 in complex with adohcy (form II) | x-ray diffraction | A | — | — |
| 3PDN | Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin | x-ray diffraction | A | — | — |
| 3PDN | Crystal structure of SMYD3 in complex with methyltransferase inhibitor sinefungin | x-ray diffraction | A | — | — |
| 3QWP | Crystal structure of SET and MYND domain containing 3; Zinc finger MYND domain-containing protein 1 | x-ray diffraction | A | — | — |
| 3QWP | Crystal structure of set and mynd domain containing 3; zinc finger mynd domain-containing protein 1 | x-ray diffraction | A | — | — |
| 3RU0 | Cocrystal structure of human SMYD3 with inhibitor Sinefungin bound | x-ray diffraction | A, B | — | — |
| 3RU0 | Cocrystal structure of human SMYD3 with inhibitor sinefungin bound | x-ray diffraction | A, B | — | — |
| 5CCL | Crystal structure of SMYD3 with SAM and oxindole compound | x-ray diffraction | A | — | — |
| 5CCM | Crystal structure of SMYD3 with SAM and EPZ030456 | x-ray diffraction | A | — | — |
| 5EX0 | Crystal structure of human SMYD3 in complex with a MAP3K2 peptide | x-ray diffraction | A | ZN | — |
| 5EX0 | Crystal structure of human SMYD3 in complex with a MAP3K2 peptide | x-ray diffraction | A | — | — |
| 5EX3 | Crystal structure of human SMYD3 in complex with a VEGFR1 peptide | x-ray diffraction | A | — | — |
| 5HI7 | Co-crystal structure of human SMYD3 with an aza-sah compound | x-ray diffraction | A | — | — |
| 5HQ8 | Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A | x-ray diffraction | A, B | ZN, MG | — |
| 5HQ8 | Co-crystal structure of human SMYD3 with a MEKK2 peptide at 2.13A | x-ray diffraction | A, B | — | — |
| 5V37 | Crystal structure of SMYD3 with SAM and EPZ028862 | x-ray diffraction | A | ZN, 8WD | — |
| 5YJO | Crystal structure of SMYD3 in complex with covalent inhibitor 4 | x-ray diffraction | A | ZN, 8W0 | — |
| 6IJL | Crystal structure of SmyD3 in complex with covalent inhibitor 5 | x-ray diffraction | A | A8U, ZN | — |
| 6IJL | Crystal structure of SMYD3 in complex with covalent inhibitor 5 | x-ray diffraction | A | A8U, ZN | — |
| 6O9O | Crystal structure of SMYD3 with potent and selective isoxazole amide inhibitor 1 | x-ray diffraction | A | ZN, LUP | — |
| 6P6G | Co-crystal structure of human SMYD3 with isoxazole amides inhibitors | x-ray diffraction | A | ZN, LUP | — |
| 6P6K | Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | x-ray diffraction | A | ZN, MG, L0J | — |
| 6P6K | Co-crystal structure of human SMYD3 with isoxazole amides inhibitors | x-ray diffraction | A | ZN, MG, L0J | — |
| 6P7Z | Co-crystal structure of human SMYD3 with isoxazole amides inhibitors | x-ray diffraction | A | ZN, O41 | — |
| 6PAF | Co-crystal structure of human SMYD3 with isoxazole amides inhibitors | x-ray diffraction | A | ZN, O6A | — |
| 6YUH | Crystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site | x-ray diffraction | A | POW, ZN | — |
| 6ZRB | Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127 | x-ray diffraction | A | QON, ZN | — |
| 7BJ1 | Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site | x-ray diffraction | A | SAM, QKT, ZN | 3 (best 0.79) |
| 7BJ1 | Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site | x-ray diffraction | A | QKT, ZN | — |
| 7O2A | X-ray structure of SMYD3 in complex with benzodiazepine-type inhibitor compound 15 | x-ray diffraction | A | UZT, ZN | — |
| 7O2B | X-ray structure of SMYD3 in complex with benzodiazepine-type inhibitor 6 | x-ray diffraction | A | UZQ, ZN | — |
| 7O2C | X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035 | x-ray diffraction | A | UZK, ZN | — |
| 7O2C | X-ray structure of SMYD3 in complex with the benzodiazepine-based probe bay-6035 | x-ray diffraction | A | UZK, ZN | — |
| 7QNR | SMYD3 in complex with fragment FL01791 | x-ray diffraction | A | SAM, ZN, E45 | 4 (best 0.80) |
| Q9H7B4 | AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) | predicted | A | — | 3 (best 0.80) |
Ligands
- ZN · Zinc ion · in 21 records
- MG · Magnesium ion · in 3 records
- A8U · Propyl (2~{R})-4-[2-[4-(1-azanylcyclopropyl) phenyl]quinolin-7-yl]carbonyl-2-methyl-piperazine-1-carboxylate · in 2 records
- L0J · N-{1-[(2-aminoethyl)sulfonyl]piperidin-4-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide · in 2 records
- LUP · 5-cyclopropyl-N-{1-[({trans-4-[(4,4,4-trifluorobutyl) amino]cyclohexyl}methyl)sulfonyl]piperidin-4-yl}-1,2-oxazole-3-carboxamide · in 2 records
- QKT · Diperodon (S-enantiomer) · in 2 records
- SAM · S-adenosylmethionine · in 2 records
- UZK · (2S)-1-[[(1R,5S)-3-azabicyclo[3.1.0]hexan-3-yl]carbonyl]-N-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide · in 2 records
- 8W0 · Propyl (3~{S})-4-[[(6~{R})-6-(aminomethyl)-5,6,7,8-tetrahydroacridin-3-yl]carbonyl]-3-methyl-piperazine-1-carboxylate · in 1 record
- 8WD · N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide · in 1 record
- E45 · 3-propan-2-yl-1,2,4-thiadiazol-5-amine · in 1 record
- O41 · 5-cyclopropyl-N-[1-(methylsulfonyl)piperidin-4-yl]-1,2-oxazole-3-carboxamide · in 1 record
- O6A · N-(1-{[4-(aminomethyl)phenyl]sulfonyl}piperidin-4-yl)-5-cyclopropyl-1,2-oxazole-3-carboxamide · in 1 record
- POW · Diperodon · in 1 record
- QON · N-[1-(2-chloroacetyl)piperidin-4-yl]-5-cyclopropyl-1,2-oxazole-3-carboxamide · in 1 record
- UZQ · (2S)-N-butyl-1-(2-fluorophenyl)carbonyl-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide · in 1 record
- UZT · (2S)-1-(4-azanylpiperidin-1-yl)carbonyl-N-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide · in 1 record
Experiment against prediction
- 7QNR chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.36 Å
- 7BJ1 chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.37 Å
- 3MEK chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.28 Å
- 3MEK chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.28 Å
- 6O9O chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.29 Å
- 6P6G chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.29 Å
- 6YUH chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.29 Å
- 5YJO chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.29 Å
- 3QWP chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.32 Å
- 3QWP chain A against the predicted model Q9H7B4: TM-score 1.00, RMSD 0.32 Å
Elsewhere
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