MolNFT v1 · #175006 · protein
Crystal structure of SETDB1 tudor domain in complexed with compound 6
7CD9 · Histone-lysine N-methyltransferase SETDB1: “Crystal structure of SETDB1 tudor domain in complexed with compound 6”. X-ray diffraction, 1 ligand (FVR), 6 pockets (best druggability 0.84). MolNFT v1 #175006 on GenesisL1: 3D structure…
- PDB
- 7CD9
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETDB1
- EC
- 2.1.1.-
- UniProt
- Q15047
- Ligands
- FVR
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone-lysine N-methyltransferase SETDB1 (EC 2.1.1.-) | protein | 215 | 15% helix, 46% strand | Q15047 |
Ligands and binding sites
- FVR · 3-methyl-2-[[(3R,5R)-1-methyl-5-(4-phenylmethoxyphenyl)piperidin-3-yl]amino]-5H-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.84 | 0.85 | 96 | FVR, CIT |
| 2 | 145 | 0.50 | 0.79 | 21 | empty |
| 3 | 155 | 0.48 | 0.77 | 19 | empty |
| 4 | 77 | 0.45 | 0.81 | 15 | empty |
| 5 | 59 | 0.44 | 0.83 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7CD9 · Crystal Structure of SETDB1 tudor domain in complexed with Compound 6 · the same entry in another collection · chain A against A, TM-score 1.00
- Q15047 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETDB1 (Q15047) · a predicted model of the same protein · chain A 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 Q15047
- Elsewhere: RCSB PDB 7CD9 · PDBe 7CD9 · UniProt Q15047
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