MolNFT v1 · #96634 · protein
2-((1H-BENZO[D]IMIDAZOL-1-YL)METHYL)-4H-PYRIDO[1,2-A]PYRIMIDIN-4-ones as novel PKM2 activators
4JPG · Pyruvate kinase isozymes M1/M2: “2-((1H-BENZO[D]IMIDAZOL-1-YL)METHYL)-4H-PYRIDO[1,2-A]PYRIMIDIN-4-ones as novel PKM2 activators”. X-ray diffraction, 2 ligands (FBP, 1OX), 20 pockets (best druggability 0.87). MolNFT v1 #96634 on…
- PDB
- 4JPG
- Type
- protein
- Length
- 2,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase isozymes M1/M2
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- FBP, 1OX
- 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 isozymes M1/M2 (EC 2.7.1.40) | protein | 519 | 39% helix, 21% strand | P14618 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 510 | 39% helix, 20% strand | P14618 |
| C | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 518 | 41% helix, 21% strand | P14618 |
| D | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 512 | 39% 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
- 1OX · 2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one · ligand · 2 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 | 352 | 0.87 | 0.96 | 41 | 1OX |
| 2 | 345 | 0.86 | 0.95 | 40 | 1OX |
| 3 | 652 | 0.85 | 0.89 | 39 | empty |
| 4 | 818 | 0.77 | 0.81 | 82 | empty |
| 5 | 267 | 0.76 | 0.89 | 37 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2905 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2891 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1358 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1238 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JPG · 2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as Novel PKM2… · 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 4JPG · PDBe 4JPG · UniProt P14618
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