Research workbench
PKM2 in complex with compound 2
Analyse PKM2 in complex with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X1V
- Type
- protein
- Length
- 2,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pkm
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- FBP, 7XX
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 512 | 38% helix, 21% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 513 | 39% helix, 21% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 518 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 511 | 40% helix, 21% strand | P14618 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- 7XX · 4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrole-2-carboxamide · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.87 | 0.96 | 38 | 7XX |
| 2 | 573 | 0.86 | 0.92 | 38 | empty |
| 3 | 342 | 0.86 | 0.95 | 43 | 7XX |
| 4 | 1012 | 0.83 | 0.84 | 130 | empty |
| 5 | 1042 | 0.75 | 0.77 | 116 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3015 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2976 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1456 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1409 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 57 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5X1V · PKM2 in complex with compound 2 · 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 5X1V · PDBe 5X1V · UniProt P14618
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