MolNFT v1 · #76061 · protein
X-ray structure of ketohexokinase in complex with a pyrimidopyrimidine analog 1
3Q92: “X-ray structure of ketohexokinase in complex with a pyrimidopyrimidine analog 1”. X-ray diffraction, 2 ligands (XNB, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #76061 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3Q92
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketohexokinase
- EC
- 2.7.1.3
- Ligands
- XNB, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketohexokinase (EC 2.7.1.3) | protein | 296 | 36% helix, 26% strand | — |
| B | Ketohexokinase (EC 2.7.1.3) | protein | 301 | 36% helix, 25% strand | — |
Ligands and binding sites
- XNB · N~8~-(cyclopropylmethyl)-N~4~-[2-(methylsulfanyl)phenyl]-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.78 | 0.83 | 65 | XNB, SO4 |
| 2 | 892 | 0.76 | 0.79 | 96 | XNB, SO4 |
| 3 | 87 | 0.43 | 0.79 | 16 | empty |
| 4 | 138 | 0.43 | 0.75 | 20 | empty |
| 5 | 109 | 0.36 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1687 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3Q92 · X-ray Structure of ketohexokinase in complex with a pyrimidopyrimidine analog 1 · 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
- Elsewhere: RCSB PDB 3Q92 · PDBe 3Q92
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