Research workbench
Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934
Analyse Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XCG
- Type
- protein
- Length
- 397 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD2
- EC
- 2.1.1.356
- UniProt
- O96028
- Ligands
- V01, UNX
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.356) | protein | 133 | 40% helix, 21% strand | O96028 |
| C | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.356) | protein | 131 | 39% helix, 21% strand | O96028 |
Ligands and binding sites
- V01 · N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl) carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide · ligand · 3 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 6 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.73 | 0.76 | 83 | UNX |
| 2 | 691 | 0.67 | 0.75 | 57 | empty |
| 3 | 117 | 0.41 | 0.75 | 21 | empty |
| 4 | 66 | 0.40 | 0.80 | 15 | V01 |
| 5 | 70 | 0.40 | 0.79 | 15 | V01 |
Interfaces
2 interfaces between chains.
- A–B · 365 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6XCG · Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934 · the same entry in another collection · chain A against A, TM-score 1.00
- O96028 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase NSD2 (O96028) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 O96028
- Elsewhere: RCSB PDB 6XCG · PDBe 6XCG · UniProt O96028
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