Research workbench
Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor arc-3353
Analyse Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HTB
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase haspin; (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-diamino-2…
- EC
- 2.7.11.1
- UniProt
- Q8TF76
- Ligands
- 66N, 6L5, NA
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase haspin (EC 2.7.11.1) | protein | 328 | 38% helix, 24% strand | Q8TF76 |
| C | (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-diamino-2,3- dihydroxycyclohexyloxy)-5-amino-2-(aminomethyl)-tetrahydro-2H-pyran- 3,4-diol | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- 66N · L-alaninamide · ligand · chains C
- 6L5 · (3R)-4-amino-3-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}-4-oxobutanoic acid (non-preferred name) · ligand · chains A, C
- NA · Sodium ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.75 | 0.83 | 61 | 6L5, MPD |
| 2 | 58 | 0.55 | 0.89 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 540 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5HTB · Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor ARC-3353 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TF76 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase haspin (Q8TF76) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8TF76
- Elsewhere: RCSB PDB 5HTB · PDBe 5HTB · UniProt Q8TF76
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