Research workbench
Crystal structure of WHSC1L1 in complex with inhibitor PEP21
Analyse Crystal structure of WHSC1L1 in complex with inhibitor PEP21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CEN
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD3; ACE-gly-val-nle-arg-ile-NH2
- EC
- 2.1.1.43
- UniProt
- Q9BZ95
- Ligands
- ACE, SAM, ZN, NH2
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 226 | 14% helix, 27% strand | Q9BZ95 |
| D | ACE-gly-val-nle-arg-ile-NH2 | protein | 5 | 0% helix, 60% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, D
- SAM · S-adenosylmethionine · ligand · chains A, D
- ZN · Zinc ion · metal · 3 copies · chains A
- NH2 · Amino group · ion · chains A, D
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 | 346 | 0.65 | 0.80 | 45 | ACE, SAM |
| 2 | 103 | 0.41 | 0.77 | 18 | empty |
| 3 | 70 | 0.33 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–D · 589 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6CEN · Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BZ95 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase NSD3 (Q9BZ95) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9BZ95
- Elsewhere: RCSB PDB 6CEN · PDBe 6CEN · UniProt Q9BZ95
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