UniProt Q9UBC3
DNA (cytosine-5)-methyltransferase 3B (Q9UBC3)
DNA (cytosine-5)-methyltransferase 3B (UniProt Q9UBC3), EC 2.1.1.37: 46 experimental structures and 1 predicted model on GenesisL1, 14 ligands bound, 141 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- Q9UBC3
- Protein
- DNA (cytosine-5)-methyltransferase 3B
- EC
- 2.1.1.37
- Experimental structures
- 46
- Predicted models
- 1
- Ligands
- 14
- Pockets
- 141 · 13 records with a druggable one
Structures
47 records of Q9UBC3 in the MolNFT archive: 46 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3FLG | The PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 beta | x-ray diffraction | A | — | — |
| 3FLG | The pwwp domain of human DNA (cytosine-5-)-methyltransferase 3 beta | x-ray diffraction | A | — | — |
| 5CIU | Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain | x-ray diffraction | A, B | — | 2 (best 0.68) |
| 5CIU | Structural basis of the recognition of H3K36ME3 by DNMT3B pwwp domain | x-ray diffraction | A, B | — | — |
| 5NR3 | Human DNMT3B PWWP domain in complex with ethambutol | x-ray diffraction | A, B | 95E, SO4 | — |
| 5NR3 | Human DNMT3B pwwp domain in complex with ethambutol | x-ray diffraction | A, B | 95E, SO4 | — |
| 5NRR | Human DNMT3B PWWP domain in complex with 5-[(2-Hydroxyethyl)(propyl)amino]-1-pentanol | x-ray diffraction | A, B | 96E, SO4 | — |
| 5NRR | Human DNMT3B pwwp domain in complex with 5-[(2-HYDROXYETHYL)(PROPYL) amino]-1-pentanol | x-ray diffraction | A, B | 96E, SO4 | — |
| 5NRS | Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine | x-ray diffraction | A, B | SO4, 962 | — |
| 5NRS | Human DNMT3B pwwp domain in complex with N,N-BIS(2-hydroxypropyl) ethanolamine | x-ray diffraction | A, B | SO4, 962 | — |
| 5NRV | Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol | x-ray diffraction | D, A | 96K, SO4 | — |
| 5NRV | Human DNMT3B pwwp domain in complex with 6-dipropylamino-1-hexanol | x-ray diffraction | D, A | 96K, SO4 | — |
| 5NV0 | Human DNMT3B pwwp domain in complex with 4-(dipropylamino) butyronitrile | x-ray diffraction | A, B | 9AH, SO4 | — |
| 5NV2 | Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S) | x-ray diffraction | A, B | 9AE, SO4 | 4 (best 0.62) |
| 5NV2 | Human DNMT3B pwwp domain in complex with N-isopropyl-1,5- dimethylhexylamine (metron S) | x-ray diffraction | A, B | 9AE, SO4 | — |
| 5NV7 | Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine | x-ray diffraction | A, B | 9AK, SO4 | 2 (best 0.63) |
| 5NV7 | Human DNMT3B pwwp domain in complex with N1-(2-hydroxyethyl)-2-methyl- 1,2-propanediamine | x-ray diffraction | A, B | 9AK, SO4 | — |
| 5NVO | Human DNMT3B PWWP domain in complex with choline | x-ray diffraction | A, B | CHT, SO4 | — |
| 5NVO | Human DNMT3B pwwp domain in complex with choline | x-ray diffraction | A, B | CHT, SO4 | — |
| 6KDA | Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site | x-ray diffraction | A, D | — | — |
| 6KDA | Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing cpgpg site | x-ray diffraction | A, D | — | — |
| 6KDB | Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpT site | x-ray diffraction | A, D | — | — |
| 6KDB | Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing cpgpt site | x-ray diffraction | A, D | — | — |
| 6KDL | Crystal structure of human DNMT3B-DNMT3L complex (I) | x-ray diffraction | A, D | — | — |
| 6KDP | Crystal structure of human DNMT3B-DNMT3L complex (II) | x-ray diffraction | A, D | — | — |
| 6KDT | Crystal structure of human DNMT3B (Q772R)-DNMT3L complex | x-ray diffraction | A, D | — | — |
| 6PA7 | The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. | electron microscopy | N, S | — | — |
| 6R3E | Human DNMT3B pwwp domain in complex with triisopropanolamine | x-ray diffraction | A, B | 96H, SO4 | — |
| 6U8P | Crystal structure of DNMT3B-DNMT3L in complex with CpGpA DNA | x-ray diffraction | A, D | MG, SAH | 10 (best 0.75) |
| 6U8P | Crystal structure of DNMT3B-DNMT3L in complex with cpgpa DNA | x-ray diffraction | A, D | MG | — |
| 6U8V | Crystal structure of DNMT3B-DNMT3L in complex with CpGpT DNA | x-ray diffraction | A, D | SAH, MG | 11 (best 0.76) |
| 6U8V | Crystal structure of DNMT3B-DNMT3L in complex with cpgpt DNA | x-ray diffraction | A, D | MG | — |
| 6U8W | Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA | x-ray diffraction | A, D | SAH, MG | 11 (best 0.73) |
| 6U8W | Crystal structure of DNMT3B(K777A)-DNMT3L in complex with cpgpt DNA | x-ray diffraction | A, D | MG | — |
| 6U8X | Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA | x-ray diffraction | A, D | MG, SAH | 9 (best 0.79) |
| 6U8X | Crystal structure of DNMT3B-DNMT3L in complex with cpapg DNA | x-ray diffraction | A, D | MG | — |
| 6U90 | Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA | x-ray diffraction | A, D | SAH | 10 (best 0.74) |
| 6U90 | Crystal structure of DNMT3B(N779A)-DNMT3L in complex with cpgpt DNA | x-ray diffraction | A, D | — | — |
| 6U91 | Crystal structure of DNMT3B(Q772R)-DNMT3L in complex with cpgpt DNA | x-ray diffraction | A, D | MG | — |
| 7O45 | Crystal structure of add domain of the human DNMT3B methyltransferase | x-ray diffraction | A, B, C, D | ZN, BR | — |
| 7V0E | Crystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain. | x-ray diffraction | A, B, C, D, E, F, G, H | SAH | 20 (best 0.76) |
| 7V0E | Crystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain. | x-ray diffraction | A, B, C, D, E, F, G, H | — | — |
| 8EIH | Cryo-EM structure of human DNMT3B homo-tetramer (form I) | electron microscopy | A, B, C, D, E | SAH, ZN | 20 (best 0.78) |
| 8EIJ | Cryo-EM structure of human DNMT3B homo-trimer | electron microscopy | A, B, D | SAH, ZN | 14 (best 0.80) |
| 8EIK | Cryo-EM structure of human DNMT3B homo-hexamer | electron microscopy | A, B, D, C, E, F | SAH, ZN | 20 (best 0.79) |
| 8XEE | Human DNMT3B mutant-R823G | x-ray diffraction | A, D | SAH | 8 (best 0.66) |
| Q9UBC3 | AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) | predicted | A | — | — |
Ligands
- SO4 · Sulfate ion · in 16 records
- SAH · S-adenosyl-L-homocysteine · in 10 records
- MG · Magnesium ion · in 9 records
- ZN · Zinc ion · in 4 records
- 95E · Ethambutol · in 2 records
- 962 · (2~{S})-1-[2-hydroxyethyl-[(2~{S})-2-oxidanylpropyl]amino]propan-2-ol · in 2 records
- 96E · 5-[2-hydroxyethyl(propyl)amino]pentan-1-ol · in 2 records
- 96K · 6-dipropylamino-1-hexanol · in 2 records
- 9AE · (2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine · in 2 records
- 9AK · N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine · in 2 records
- CHT · Choline ion · in 2 records
- 96H · Triisopropanolamine · in 1 record
- 9AH · 4-(dipropylamino)butanenitrile · in 1 record
- BR · Bromide ion · in 1 record
Experiment against prediction
- 6U8P chain A against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.52 Å
- 6U8X chain A against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.53 Å
- 8XEE chain A against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.58 Å
- 6U8X chain D against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.55 Å
- 6U8P chain D against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.55 Å
- 6U8V chain A against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.56 Å
- 7V0E chain A against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.54 Å
- 6U8W chain A against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.57 Å
- 6U8V chain D against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.56 Å
- 8XEE chain D against the predicted model Q9UBC3: TM-score 0.99, RMSD 0.64 Å
Elsewhere
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