MolNFT v1 · #114504 · protein
Crystal structure of trypanosoma cruzi glucokinase in complex with inhibitor dbt-glcn
5BRH · Glucokinase 1, putative: “Crystal structure of trypanosoma cruzi glucokinase in complex with inhibitor dbt-glcn”. X-ray diffraction, 1 ligand (4V3), 12 pockets (best druggability 0.73). MolNFT v1 #114504 on GenesisL1: 3D structure…
- PDB
- 5BRH
- Type
- protein
- Length
- 731 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase 1, putative
- EC
- 2.7.1.2
- UniProt
- Q4E4E1
- Ligands
- 4V3
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase 1, putative (EC 2.7.1.2) | protein | 367 | 42% helix, 24% strand | Q4E4E1 |
| B | Glucokinase 1, putative (EC 2.7.1.2) | protein | 364 | 44% helix, 24% strand | Q4E4E1 |
Ligands and binding sites
- 4V3 · 2-deoxy-2-({[(1,1-dioxido-1-benzothiophen-2-yl)methoxy]carbonyl}amino)-beta-D-glucopyranose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.73 | 0.99 | 21 | empty |
| 2 | 602 | 0.71 | 0.79 | 66 | 4V3 |
| 3 | 590 | 0.70 | 0.79 | 67 | 4V3 |
| 4 | 167 | 0.69 | 0.88 | 34 | empty |
| 5 | 100 | 0.52 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1964 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5BRH · Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor DBT-GlcN · 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 Q4E4E1
- Elsewhere: RCSB PDB 5BRH · PDBe 5BRH · UniProt Q4E4E1
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