UniProt P26358
DNA (cytosine-5)-methyltransferase 1 (P26358)
DNA (cytosine-5)-methyltransferase 1 (UniProt P26358), EC 2.1.1.37: 31 experimental structures and 1 predicted model on GenesisL1, 9 ligands bound, 81 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- P26358
- Protein
- DNA (cytosine-5)-methyltransferase 1
- EC
- 2.1.1.37
- Experimental structures
- 31
- Predicted models
- 1
- Ligands
- 9
- Pockets
- 81 · 8 records with a druggable one
Structures
32 records of P26358 in the MolNFT archive: 31 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3EPZ | Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 | x-ray diffraction | A, B | — | — |
| 3EPZ | Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 | x-ray diffraction | A, B | — | — |
| 3PTA | Crystal structure of human DNMT1(646-1600) in complex with DNA | x-ray diffraction | A | — | — |
| 3PTA | Crystal structure of human DNMT1(646-1600) in complex with DNA | x-ray diffraction | A | — | — |
| 3SWR | Structure of human DNMT1 (601-1600) in complex with Sinefungin | x-ray diffraction | A | — | — |
| 3SWR | Structure of human DNMT1 (601-1600) in complex with sinefungin | x-ray diffraction | A | — | — |
| 4WXX | The crystal structure of human DNMT1(351-1600) | x-ray diffraction | A, B | — | — |
| 4YOC | Crystal Structure of human DNMT1 and USP7/HAUSP complex | x-ray diffraction | A | — | — |
| 4YOC | Crystal structure of human DNMT1 and USP7/HAUSP complex | x-ray diffraction | A | — | — |
| 4Z96 | Crystal structure of DNMT1 in complex with USP7 | x-ray diffraction | C | — | — |
| 4Z96 | Crystal structure of DNMT1 in complex with USP7 | x-ray diffraction | C | — | — |
| 5WVO | Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 | x-ray diffraction | C | ZN | 3 (best 0.68) |
| 5WVO | Crystal structure of DNMT1 rfts domain in complex with K18/K23 mono- ubiquitylated histone H3 | x-ray diffraction | C | ZN | — |
| 5YDR | Structure of DNMT1 RFTS domain in complex with ubiquitin | x-ray diffraction | B | ZN, PO4 | 4 (best 0.69) |
| 5YDR | Structure of DNMT1 rfts domain in complex with ubiquitin | x-ray diffraction | B | ZN, PO4 | — |
| 6L1F | Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1 | x-ray diffraction | A | — | — |
| 6L1F | Crystal structure of PHF20L1 TUDOR1 in complex with K142ME1 DNMT1 | x-ray diffraction | A | — | — |
| 6X9I | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA | x-ray diffraction | A | SAH, ZN | 13 (best 0.82) |
| 6X9I | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna | x-ray diffraction | A | ZN | — |
| 6X9J | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 | x-ray diffraction | A | ZN, X52 | 11 (best 0.83) |
| 6X9J | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3830052 | x-ray diffraction | A | ZN, X52 | — |
| 6X9K | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3685032A | x-ray diffraction | A | ZN, UXM | — |
| 7SFC | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A | x-ray diffraction | A | ZN, I67 | 10 (best 0.83) |
| 7SFC | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3735967A | x-ray diffraction | A | ZN, I67 | — |
| 7SFE | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3830334A | x-ray diffraction | A | ZN, 96I | — |
| 7SFF | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B | x-ray diffraction | A | ZN, C79 | 10 (best 0.83) |
| 7SFF | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3852279B | x-ray diffraction | A | ZN, C79 | — |
| 7SFG | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM | x-ray diffraction | A | ZN, SAM | 13 (best 0.77) |
| 7SFG | Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and cofactor SAM | x-ray diffraction | A | ZN | — |
| 7XI9 | Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated… | electron microscopy | A | ZN, SAH | 15 (best 0.73) |
| 8V9U | Solution NMR structure of human DNMT1 N-terminal alpha-helical domain | solution nmr | A | — | 2 (best 0.40) |
| P26358 | AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (P26358) | predicted | A | — | — |
Ligands
- ZN · Zinc ion · in 17 records
- C79 · (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl) phenyl]acetamide · in 2 records
- I67 · N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl) phenyl]methyl}glycinamide · in 2 records
- PO4 · Phosphate ion · in 2 records
- SAH · S-adenosyl-L-homocysteine · in 2 records
- X52 · N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino) ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide · in 2 records
- 96I · (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]amino}-2-phenylacetamide · in 1 record
- SAM · S-adenosylmethionine · in 1 record
- UXM · (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide · in 1 record
Experiment against prediction
- 4WXX chain A against the predicted model P26358: TM-score 0.99, RMSD 1.04 Å
- 4WXX chain B against the predicted model P26358: TM-score 0.99, RMSD 1.14 Å
- 4YOC chain A against the predicted model P26358: TM-score 0.99, RMSD 1.52 Å
- 4YOC chain A against the predicted model P26358: TM-score 0.99, RMSD 1.52 Å
- 7SFC chain A against the predicted model P26358: TM-score 0.98, RMSD 1.64 Å
- 7SFC chain A against the predicted model P26358: TM-score 0.98, RMSD 1.64 Å
- 7SFF chain A against the predicted model P26358: TM-score 0.98, RMSD 1.66 Å
- 7SFF chain A against the predicted model P26358: TM-score 0.98, RMSD 1.66 Å
- 7SFE chain A against the predicted model P26358: TM-score 0.98, RMSD 1.68 Å
- 6X9K chain A against the predicted model P26358: TM-score 0.98, RMSD 1.70 Å
Elsewhere
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