MolNFT v1 · #165378 · protein
PKM2 in complex with compound 5
6TTF · Pyruvate kinase pkm: “PKM2 in complex with compound 5”. Electron microscopy, 2 ligands (LZ2, FBP), 20 pockets (best druggability 0.86). MolNFT v1 #165378 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TTF
- Type
- protein
- Length
- 2,056 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pkm
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- LZ2, FBP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 514 | 38% helix, 20% strand | P14618 |
Ligands and binding sites
- LZ2 · 5-hydroxynaphthalene-1-sulfonamide · ligand · 4 copies · chains A, B, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.86 | 0.94 | 60 | LZ2 |
| 2 | 415 | 0.86 | 0.93 | 56 | LZ2 |
| 3 | 785 | 0.84 | 0.87 | 86 | empty |
| 4 | 713 | 0.70 | 0.77 | 76 | empty |
| 5 | 731 | 0.69 | 0.76 | 75 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2685 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2685 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1469 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1463 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 42 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6TTF · PKM2 in complex with Compound 5 · the same entry in another collection · chain A against A, TM-score 1.00
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 P14618
- Elsewhere: RCSB PDB 6TTF · PDBe 6TTF · UniProt P14618
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