Research workbench
PKM2 in complex with compound 10
Analyse PKM2 in complex with compound 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TTQ
- Type
- protein
- Length
- 2,040 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
- NXH, FBP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 510 | 36% helix, 22% strand | P14618 |
Ligands and binding sites
- NXH · 1-propan-2-yl-3-pyridin-4-yl-urea · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.89 | 0.90 | 136 | NXH |
| 2 | 1067 | 0.88 | 0.89 | 117 | NXH |
| 3 | 1192 | 0.78 | 0.80 | 106 | empty |
| 4 | 1033 | 0.76 | 0.78 | 99 | empty |
| 5 | 690 | 0.71 | 0.78 | 60 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2880 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2879 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1026 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1019 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TTQ · PKM2 in complex with Compound 10 · 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 6TTQ · PDBe 6TTQ · UniProt P14618
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