MolNFT v1 · #79038 · protein
A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase
3SRK: “A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase”. X-ray diffraction, 3 ligands (LSA, PTK, K), 10 pockets (best druggability 0.84). MolNFT v1 #79038 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3SRK
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- LSA, PTK, K
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 493 | 41% helix, 22% strand | Q27686 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 405 | 46% helix, 16% strand | Q27686 |
Ligands and binding sites
- LSA · 1,2-benzisothiazol-3(2H)-one 1,1-dioxide · ligand · 2 copies · chains A, B
- PTK · pyrene-1,3,6,8-tetrasulfonic acid · ligand · chains A
- K · Potassium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.84 | 0.96 | 31 | empty |
| 2 | 776 | 0.71 | 0.77 | 78 | LSA, K |
| 3 | 259 | 0.56 | 0.78 | 24 | empty |
| 4 | 277 | 0.55 | 0.76 | 45 | LSA, K |
| 5 | 253 | 0.54 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2346 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3SRK · A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase · the same entry in another collection · chain A against A, TM-score 1.00
- Q27686 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q27686) · a predicted model of the same protein · chain B 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 Q27686
- Elsewhere: RCSB PDB 3SRK · PDBe 3SRK · UniProt Q27686
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