UniProt Q9Y5A9
YTH domain-containing family protein 2 (Q9Y5A9)
YTH domain-containing family protein 2 (UniProt Q9Y5A9): 46 experimental structures and 1 predicted model on GenesisL1, 22 ligands bound, 56 pockets. Binding sites, druggability and experiment against prediction (TM-score) in…
- UniProt
- Q9Y5A9
- Protein
- YTH domain-containing family protein 2
- Experimental structures
- 46
- Predicted models
- 1
- Ligands
- 22
- Pockets
- 56 · 12 records with a druggable one
Structures
47 records of Q9Y5A9 in the MolNFT archive: 46 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 4RDN | Structure of YTH-YTHDF2 in complex with m6A | x-ray diffraction | A, B | — | — |
| 4RDN | Structure of yth-YTHDF2 in complex with M6A | x-ray diffraction | A, B | — | — |
| 4RDO | Structure of YTH-YTHDF2 in the free state | x-ray diffraction | A, B, C, D, E, F | — | — |
| 4RDO | Structure of yth-YTHDF2 in the free state | x-ray diffraction | A, B, C, D, E, F | — | — |
| 4WQN | Crystal structure of N6-methyladenosine RNA reader YTHDF2 | x-ray diffraction | A, B | — | — |
| 4WQN | Crystal structure of N6-methyladenosine RNA reader YTHDF2 | x-ray diffraction | A, B | — | — |
| 7A1V | Crystal structure of YTHDF2 in complex with m1A | x-ray diffraction | A, B | M1A, SO4 | 4 (best 0.53) |
| 7A1V | Crystal structure of YTHDF2 in complex with M1A | x-ray diffraction | A, B | M1A, SO4 | — |
| 7BIK | Crystal structure of YTHDF2 in complex with m6Am | x-ray diffraction | A, B | SO4, TV8 | 3 (best 0.50) |
| 7BIK | Crystal structure of YTHDF2 in complex with M6AM | x-ray diffraction | A, B | SO4, TV8 | — |
| 7R5F | Crystal structure of YTHDF2 with compound YLI_DF_012 | x-ray diffraction | A, B | SO4, CL, I3V | 2 (best 0.51) |
| 7R5F | Crystal structure of YTHDF2 with compound YLI_DF_012 | x-ray diffraction | A, B | SO4, CL, I3V | — |
| 7R5L | Crystal structure of YTHDF2 with compound YLI_DC1_015 | x-ray diffraction | A | I4S, SO4 | — |
| 7R5L | Crystal structure of YTHDF2 with compound YLI_DC1_015 | x-ray diffraction | A | I4S, SO4 | — |
| 7R5W | Crystal structure of YTHDF2 with compound YLI_DF_029 | x-ray diffraction | A, B | SO4, I5Z, CL | 3 (best 0.54) |
| 7R5W | Crystal structure of YTHDF2 with compound YLI_DF_029 | x-ray diffraction | A, B | SO4, I5Z, CL | — |
| 7YWB | Crystal structure of YTHDF2 in complex with N6-Methyladenine | x-ray diffraction | A, B | SO4, N6M, CL | 3 (best 0.45) |
| 7YWB | Crystal structure of YTHDF2 in complex with N6-methyladenine | x-ray diffraction | A, B | SO4, N6M, CL | — |
| 7YX6 | Crystal structure of YTHDF2 with compound YLI_DF_027 | x-ray diffraction | A, B | SO4, I6R | 3 (best 0.53) |
| 7YX6 | Crystal structure of YTHDF2 with compound YLI_DF_027 | x-ray diffraction | A, B | SO4, I6R | — |
| 7YXE | Crystal structure of YTHDF2 with compound ZA_143 | x-ray diffraction | A, B | I82, SO4, NA | 3 (best 0.50) |
| 7YXE | Crystal structure of YTHDF2 with compound ZA_143 | x-ray diffraction | A, B | I82, SO4, NA | — |
| 7Z26 | Crystal structure of YTHDF2 YTH domain in complex with m6A RNA | x-ray diffraction | A, B | SO4 | 2 (best 0.39) |
| 7Z26 | Crystal structure of YTHDF2 yth domain in complex with M6A RNA | x-ray diffraction | A, B | SO4 | 2 (best 0.39) |
| 7Z4U | Crystal structure of YTHDF2 with compound YLI_DF_028 | x-ray diffraction | A, B | SO4, CL, FIQ | 2 (best 0.56) |
| 7Z4U | Crystal structure of YTHDF2 with compound YLI_DF_028 | x-ray diffraction | A, B | SO4, CL, FIQ | 2 (best 0.56) |
| 7Z54 | Crystal structure of YTHDF2 with compound YLI_DC1_006 | x-ray diffraction | A, B | SO4, CL, OYT | 2 (best 0.46) |
| 7Z54 | Crystal structure of YTHDF2 with compound YLI_DC1_006 | x-ray diffraction | A, B | SO4, CL, OYT | 2 (best 0.46) |
| 7Z5M | Crystal structure of YTHDF2 with compound YLI_DC1_008 | x-ray diffraction | A, B | SO4, CL, 5ZK | 3 (best 0.52) |
| 7Z5M | Crystal structure of YTHDF2 with compound YLI_DC1_008 | x-ray diffraction | A, B | SO4, CL, 5ZK | — |
| 7Z7B | Crystal structure of YTHDF2 with compound YLI_DC1_003 | x-ray diffraction | A, B | SO4, CL, OYK | 2 (best 0.49) |
| 7Z7B | Crystal structure of YTHDF2 with compound YLI_DC1_003 | x-ray diffraction | A, B | SO4, CL, OYK | — |
| 7Z7F | Crystal structure of YTHDF2 with compound YLI_DC1_005 | x-ray diffraction | A, B | SO4, CL, IF3 | 3 (best 0.51) |
| 7Z7F | Crystal structure of YTHDF2 with compound YLI_DC1_005 | x-ray diffraction | A, B | SO4, CL, IF3 | — |
| 7Z8P | Crystal structure of YTHDF2 with compound ZA_166 | x-ray diffraction | A, B | SO4, IFZ | 2 (best 0.46) |
| 7Z8P | Crystal structure of YTHDF2 with compound ZA_166 | x-ray diffraction | A, B | SO4, IFZ | — |
| 7Z8W | Crystal structure of YTHDF2 with compound YLI_DC1_018 | x-ray diffraction | A, B | SO4, IHR, CL | 2 (best 0.52) |
| 7Z8W | Crystal structure of YTHDF2 with compound YLI_DC1_018 | x-ray diffraction | A, B | SO4, IHR, CL | — |
| 7Z8X | Crystal structure of YTHDF2 with compound YLI_DC1_017 | x-ray diffraction | A, B | IGX, SO4 | 4 (best 0.44) |
| 7Z8X | Crystal structure of YTHDF2 with compound YLI_DC1_017 | x-ray diffraction | A, B | IGX, SO4 | — |
| 7Z92 | Crystal structure of YTHDF2 with compound YLI_DF_024 | x-ray diffraction | A, B | SO4, IGT | 2 (best 0.47) |
| 7Z92 | Crystal structure of YTHDF2 with compound YLI_DF_024 | x-ray diffraction | A, B | SO4, IGT | — |
| 7Z93 | Crystal structure of YTHDF2 with compound YLI_DF_022 | x-ray diffraction | A, B | CL, SO4, IHF | 2 (best 0.51) |
| 7Z93 | Crystal structure of YTHDF2 with compound YLI_DF_022 | x-ray diffraction | A, B | CL, SO4, IHF | — |
| 7ZG4 | Crystal structure of YTHDF2 with compound YLI_DF_042 | x-ray diffraction | A, B | SO4, IQL | 2 (best 0.53) |
| 7ZG4 | Crystal structure of YTHDF2 with compound YLI_DF_042 | x-ray diffraction | A, B | SO4, IQL | — |
| Q9Y5A9 | AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) | predicted | A | — | 1 (best 0.41) |
Ligands
- SO4 · Sulfate ion · in 40 records
- CL · Chloride ion · in 20 records
- 5ZK · ~{N},3-dimethyl-1~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · in 2 records
- FIQ · 6-cyclopropyl-3-methyl-1H-pyrimidine-2,4-dione · in 2 records
- I3V · 5-azanyl-6-methyl-1~{H}-pyrimidine-2,4-dione · in 2 records
- I4S · 3,6-dimethyl-2~{H}-1,2,4-triazin-5-one · in 2 records
- I5Z · 6-cyclopropyl-1H-pyrimidine-2,4-dione · in 2 records
- I6R · 6-ethyl-1H-pyrimidine-2,4-dione · in 2 records
- I82 · ~{N}-methyl-3-phenyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · in 2 records
- IF3 · ~{N}2,~{N}6,9-trimethylpurine-2,6-diamine · in 2 records
- IFZ · 3-bromanyl-~{N}-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · in 2 records
- IGT · 5-azanyl-3,6-dimethyl-1H-pyrimidine-2,4-dione · in 2 records
- IGX · 6-methoxy-1H-pyrimidine-2,4-dione · in 2 records
- IHF · 5-azanyl-6-ethyl-1H-pyrimidine-2,4-dione · in 2 records
- IHR · ~{N}-cyclopropyl-3-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · in 2 records
- IQL · N-methylpyrimidine-2-carboximidamide · in 2 records
- M1A · 6-amino-1-methylpurine · in 2 records
- N6M · N-methyl-9H-purin-6-amine · in 2 records
- NA · Sodium ion · in 2 records
- OYK · ~{N},9-dimethylpurin-6-amine · in 2 records
- OYT · 9-cyclopropyl-~{N}-methyl-purin-6-amine · in 2 records
- TV8 · (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol · in 2 records
Experiment against prediction
- 4WQN chain A against the predicted model Q9Y5A9: TM-score 0.98, RMSD 0.82 Å
- 4WQN chain A against the predicted model Q9Y5A9: TM-score 0.98, RMSD 0.82 Å
- 4RDO chain F against the predicted model Q9Y5A9: TM-score 0.97, RMSD 0.92 Å
- 4RDO chain F against the predicted model Q9Y5A9: TM-score 0.97, RMSD 0.92 Å
- 4RDO chain E against the predicted model Q9Y5A9: TM-score 0.97, RMSD 0.93 Å
- 4RDO chain E against the predicted model Q9Y5A9: TM-score 0.97, RMSD 0.93 Å
- 7Z8W chain A against the predicted model Q9Y5A9: TM-score 0.97, RMSD 1.28 Å
- 7Z8W chain A against the predicted model Q9Y5A9: TM-score 0.97, RMSD 1.28 Å
- 4RDO chain B against the predicted model Q9Y5A9: TM-score 0.96, RMSD 1.00 Å
- 4RDO chain B against the predicted model Q9Y5A9: TM-score 0.96, RMSD 1.00 Å
Elsewhere
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