Research workbench
Human PFKFB3 in complex with a pyrrolopyrimidone compound
Analyse Human PFKFB3 in complex with a pyrrolopyrimidone compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D4M
- Type
- protein
- Length
- 439 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase 3
- EC
- 2.7.1.105, 3.1.3.46
- UniProt
- Q16875
- Ligands
- PHS, F6P, BKV, PO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase 3 (EC 2.7.1.105, 3.1.3.46) | protein | 439 | 42% helix, 17% strand | Q16875 |
Ligands and binding sites
- PHS · Phosphonic acid · ligand · chains A
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · chains A
- BKV · 7-(4-bromophenyl)-5-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.78 | 0.88 | 44 | PO4 |
| 2 | 212 | 0.75 | 0.90 | 43 | PHS, F6P |
| 3 | 321 | 0.73 | 0.85 | 45 | BKV |
| 4 | 82 | 0.34 | 0.75 | 19 | empty |
Compared structures
- 4D4M · human PFKFB3 in complex with a pyrrolopyrimidone compound · the same entry in another collection · chain A against A, TM-score 1.00
- Q16875 · AlphaFold monomer V2.0 prediction for 6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q16875
- Elsewhere: RCSB PDB 4D4M · PDBe 4D4M · UniProt Q16875
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