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Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor ARC-3372
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
- 5HTC
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Serine/threonine-protein kinase haspin; Arc-3372 inhibitor
- EC
- 2.7.11.1
- UniProt
- Q8TF76
- Ligands
- 66M, NA
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.5 · 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 | Arc-3372 inhibitor | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- 66M · (2R)-2-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}butanedioic acid (non-preferred name) · ligand · chains A, C
- NA · Sodium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.76 | 0.83 | 64 | 66M |
Interfaces
1 interface between chains.
- A–C · 520 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HTC · Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor arc-3372 · 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 5HTC · PDBe 5HTC · UniProt Q8TF76
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