Research workbench
Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor
Analyse Methyltransferase domain of human suppressor of variegation 3-9 homolog 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P0R
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SUV39H2
- EC
- 2.1.1.43
- UniProt
- Q9H5I1
- Ligands
- NM4, ZN, UNX
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SUV39H2 (EC 2.1.1.43) | protein | 255 | 14% helix, 26% strand | Q9H5I1 |
| B | Histone-lysine N-methyltransferase SUV39H2 (EC 2.1.1.43) | protein | 230 | 15% helix, 26% strand | Q9H5I1 |
Ligands and binding sites
- NM4 · (3S)-1-[2-(5-chloro-2,4-dimethoxyphenyl)imidazo[1,2-a]pyridin-7-yl]-N-[(pyridin-4-yl)methyl]pyrrolidin-3-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 7 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.74 | 0.79 | 83 | empty |
| 2 | 100 | 0.58 | 0.85 | 22 | NM4 |
| 3 | 155 | 0.55 | 0.81 | 28 | NM4 |
| 4 | 222 | 0.51 | 0.76 | 32 | empty |
| 5 | 76 | 0.40 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 422 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6P0R · Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H5I1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SUV39H2 (Q9H5I1) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9H5I1
- Elsewhere: RCSB PDB 6P0R · PDBe 6P0R · UniProt Q9H5I1
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