Research workbench
Structure of human SETD8 in complex with covalent inhibitor MS4138
Analyse Structure of human SETD8 in complex with covalent inhibitor MS4138 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BOZ
- Type
- protein
- Length
- 273 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase KMT5A
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NQR1
- Ligands
- E1J
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43) | protein | 139 | 17% helix, 40% strand | Q9NQR1 |
| B | N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43) | protein | 134 | 16% helix, 42% strand | Q9NQR1 |
Ligands and binding sites
- E1J · N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl) quinazolin-4-yl]amino}propyl)prop-2-enamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.80 | 0.88 | 57 | EDO, E1J |
| 2 | 108 | 0.40 | 0.76 | 18 | empty |
| 3 | 71 | 0.37 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1103 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6BOZ · Structure of human SETD8 in complex with covalent inhibitor MS4138 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQR1 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase KMT5A (Q9NQR1) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q9NQR1
- Elsewhere: RCSB PDB 6BOZ · PDBe 6BOZ · UniProt Q9NQR1
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