UniProt Q9BYW2
Histone-lysine N-methyltransferase SETD2 (Q9BYW2)
Histone-lysine N-methyltransferase SETD2 (UniProt Q9BYW2), EC 2.1.1.-, 2.1.1.359: 58 experimental structures and 1 predicted model on GenesisL1, 16 ligands bound, 48 pockets. Binding sites, druggability and experiment against…
- UniProt
- Q9BYW2
- Protein
- Histone-lysine N-methyltransferase SETD2
- EC
- 2.1.1.-, 2.1.1.359, 2.1.1.43
- Experimental structures
- 58
- Predicted models
- 1
- Ligands
- 16
- Pockets
- 48 · 17 records with a druggable one
Structures
59 records of Q9BYW2 in the MolNFT archive: 58 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 2A7O | Solution Structure of the hSet2/HYPB SRI domain | solution nmr | A | — | — |
| 2A7O | Solution structure of the HSET2/HYPB sri domain | solution nmr | A | — | — |
| 2MDC | Solution structure of the WW domain of HYPB | solution nmr | A | — | — |
| 2MDC | Solution structure of the ww domain of hypb | solution nmr | A | — | — |
| 2MDI | Solution structure of the PP2WW mutant (KPP2WW) of HYPB | solution nmr | A | — | — |
| 2MDI | Solution structure of the PP2WW mutant (KPP2WW) of hypb | solution nmr | A | — | — |
| 2MDJ | Solution structure of WW domain with polyproline stretch (PP2WW) of HYPB | solution nmr | A | — | — |
| 2MDJ | Solution structure of ww domain with polyproline stretch (PP2WW) of hypb | solution nmr | A | — | — |
| 4FMU | Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound… | x-ray diffraction | A | — | — |
| 4FMU | Crystal structure of methyltransferase domain of human set domain- containing protein 2 compound… | x-ray diffraction | A | — | — |
| 4H12 | The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in… | x-ray diffraction | A | — | — |
| 4H12 | The crystal structure of methyltransferase domain of human set domain- containing protein 2 in… | x-ray diffraction | A | — | — |
| 5JJY | Crystal structure of SETD2 bound to histone H3.3 K36M peptide | x-ray diffraction | A | ZN, SAH, SCN | 2 (best 0.68) |
| 5JJY | Crystal structure of SETD2 bound to histone H3.3 K36M peptide | x-ray diffraction | A | — | — |
| 5JLB | Crystal structure of SETD2 bound to histone H3.3 K36I peptide | x-ray diffraction | A | SCN, ZN | — |
| 5JLB | Crystal structure of SETD2 bound to histone H3.3 K36I peptide | x-ray diffraction | A | — | — |
| 5JLE | Crystal structure of SETD2 bound to SAH | x-ray diffraction | A | ZN | — |
| 5JLE | Crystal structure of SETD2 bound to sah | x-ray diffraction | A | — | — |
| 5LSS | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A | ZN, SCN, 76H | 3 (best 0.66) |
| 5LSS | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A | ZN, SCN | — |
| 5LSX | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A | ZN, 76O | 3 (best 0.69) |
| 5LSX | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A | ZN, 76O | — |
| 5LSY | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A | ZN, SCN, 76M | 4 (best 0.68) |
| 5LSY | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A | ZN, SCN, 76M | — |
| 5LSZ | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A | ZN, SCN, 76K | — |
| 5LSZ | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A | ZN, SCN, 76K | — |
| 5LT6 | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A, B | ZN, SCN, 76J | 5 (best 0.67) |
| 5LT6 | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A, B | ZN, SCN, 76J | — |
| 5LT7 | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A | ZN, SCN, 76L | — |
| 5LT7 | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A | ZN, SCN, 76L | — |
| 5LT8 | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | x-ray diffraction | A | ZN | — |
| 5LT8 | Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives | x-ray diffraction | A | ZN | — |
| 5V21 | Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM | x-ray diffraction | A | ZN, SAM | 2 (best 0.64) |
| 5V21 | Crystal structure of human SETD2 set-domain in complex with H3K36M peptide and SAM | x-ray diffraction | A | ZN | — |
| 5V22 | Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAH | x-ray diffraction | A | ZN, SAH | 2 (best 0.67) |
| 5V22 | Crystal structure of human SETD2 set-domain in complex with H3K36M peptide and sah | x-ray diffraction | A | ZN | — |
| 6J9J | crystal structure of SESTD2 in complex with H3.3S31phK36M peptide | x-ray diffraction | A | ZN, SAH, SCN | 2 (best 0.65) |
| 6J9J | Crystal structure of SESTD2 in complex with H3.3S31PHK36M peptide | x-ray diffraction | A | ZN, SCN | — |
| 6VDB | SETD2 in complex with a H3-variant super-substrate peptide | x-ray diffraction | A | UNX, ZN, SCN | — |
| 7EA8 | Human SETD2 bound to a nucleosome containing oncohistone mutations | electron microscopy | L | ZN, SAM | 5 (best 0.79) |
| 7EA8 | Human SETD2 bound to a nucleosome containing oncohistone mutations | electron microscopy | L | ZN | — |
| 7EVR | Crystal structure of hnRNP L RRM2 in complex with SETD2 | x-ray diffraction | B, D | — | — |
| 7EVR | Crystal structure of hnrnp L RRM2 in complex with SETD2 | x-ray diffraction | B, D | — | — |
| 7EVS | Crystal structure of hnRNP LL RRM2 in complex with SETD2 | x-ray diffraction | C, D | — | — |
| 7EVS | Crystal structure of hnrnp ll RRM2 in complex with SETD2 | x-ray diffraction | C, D | — | — |
| 7LZB | Crystal Structure of SETD2 bound to Compound 2 | x-ray diffraction | A | ZN, SAM, YJ1 | 2 (best 0.75) |
| 7LZB | Crystal structure of SETD2 bound to compound 2 | x-ray diffraction | A | ZN, YJ1 | — |
| 7LZD | Crystal Structure of SETD2 bound to Compound 35 | x-ray diffraction | A | ZN, SAM, YHY | 2 (best 0.75) |
| 7LZD | Crystal structure of SETD2 bound to compound 35 | x-ray diffraction | A | ZN, YHY | — |
| 7LZF | Crystal Structure of SETD2 bound to Compound 57 | x-ray diffraction | A | ZN, YHV | — |
| 7LZF | Crystal structure of SETD2 bound to compound 57 | x-ray diffraction | A | ZN, YHV | — |
| 7TY2 | Crystal Structure of SETD2 Bound to an Indole-based Inhibitor | x-ray diffraction | A | ZN, SAM, KS6 | 2 (best 0.76) |
| 7TY2 | Crystal structure of SETD2 bound to an indole-based inhibitor | x-ray diffraction | A | ZN, KS6 | — |
| 7TY3 | Crystal structure of SETD2 bound to an indole-based inhibitor | x-ray diffraction | A | ZN, SAM, KRF | 2 (best 0.75) |
| 8Q5P | Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from human… | x-ray diffraction | A | ZN, SAM | 2 (best 0.65) |
| 9EGZ | RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 | electron microscopy | l | ZN | 2 (best 0.79) |
| 9EH1 | RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream | electron microscopy | l | — | 1 (best 0.79) |
| 9EH2 | RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream | electron microscopy | l | — | — |
| Q9BYW2 | AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD2 (Q9BYW2) | predicted | A | — | 7 (best 0.85) |
Ligands
- ZN · Zinc ion · in 37 records
- SCN · Thiocyanate ion · in 15 records
- SAM · S-adenosylmethionine · in 7 records
- SAH · S-adenosyl-L-homocysteine · in 3 records
- 76J · [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium · in 2 records
- 76K · [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(3-oxidanylpropyl)azanium · in 2 records
- 76L · [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-[(2~{R})-2-oxidanylpropyl]azanium · in 2 records
- 76M · [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(2-methylpropyl)azanium · in 2 records
- 76O · [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium · in 2 records
- KS6 · N-[(1R,3S)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide · in 2 records
- YHV · 4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl) (methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide · in 2 records
- YHY · N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-carboxamide · in 2 records
- YJ1 · N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide · in 2 records
- 76H · [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-propyl-azanium · in 1 record
- KRF · N-[(1R,3R)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide · in 1 record
- UNX · Unknown atom or ion · in 1 record
Experiment against prediction
- 5V22 chain A against the predicted model Q9BYW2: TM-score 1.00, RMSD 0.36 Å
- 6J9J chain A against the predicted model Q9BYW2: TM-score 1.00, RMSD 0.37 Å
- 5JJY chain A against the predicted model Q9BYW2: TM-score 1.00, RMSD 0.38 Å
- 5V21 chain A against the predicted model Q9BYW2: TM-score 1.00, RMSD 0.39 Å
- 5JLB chain A against the predicted model Q9BYW2: TM-score 0.99, RMSD 0.36 Å
- 5JLB chain A against the predicted model Q9BYW2: TM-score 0.99, RMSD 0.36 Å
- 5V22 chain A against the predicted model Q9BYW2: TM-score 0.99, RMSD 0.36 Å
- 6J9J chain A against the predicted model Q9BYW2: TM-score 0.99, RMSD 0.37 Å
- 5JJY chain A against the predicted model Q9BYW2: TM-score 0.99, RMSD 0.38 Å
- 5V21 chain A against the predicted model Q9BYW2: TM-score 0.99, RMSD 0.39 Å
Elsewhere
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