Research workbench
PKM2 in complex with compound 6
Analyse PKM2 in complex with compound 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TTI
- Type
- protein
- Length
- 1,664 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
- NXE, FBP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 416 | 46% helix, 16% strand | P14618 |
Ligands and binding sites
- NXE · ~{N}-[3-(trifluoromethyl)-1,2-oxazol-5-yl]ethanamide · 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
- DMS · Dimethyl sulfoxide · additive · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.87 | 0.92 | 78 | NXE, DMS |
| 2 | 1042 | 0.86 | 0.87 | 109 | NXE, DMS |
| 3 | 478 | 0.82 | 0.89 | 36 | empty |
| 4 | 297 | 0.76 | 0.88 | 48 | empty |
| 5 | 539 | 0.75 | 0.83 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2695 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2693 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1486 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1481 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 40 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6TTI · PKM2 in complex with Compound 6 · 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 6TTI · PDBe 6TTI · UniProt P14618
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