Research workbench
Thermodynamic and structure guided design of statin hmg-coa reductase inhibitors
Analyse Thermodynamic and structure guided design of statin hmg-coa reductase inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CD0
- Type
- protein
- Length
- 1,652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- 3-hydroxy-3-methylglutaryl-coenzyme A reductase
- EC
- 1.1.1.34
- UniProt
- P04035
- Ligands
- 6HI
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) | protein | 421 | 45% helix, 22% strand | P04035 |
| C | 3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) | protein | 414 | 46% helix, 22% strand | P04035 |
| D | 3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) | protein | 396 | 44% helix, 24% strand | P04035 |
Ligands and binding sites
- 6HI · (3R,5R)-7-{2-[(4-fluorobenzyl)carbamoyl]-4-(4-fluorophenyl)-1-(1-methylethyl)-1H-imidazol-5-yl}-3,5-dihydroxyheptanoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.74 | 0.81 | 64 | empty |
| 2 | 488 | 0.72 | 0.82 | 61 | 6HI |
| 3 | 493 | 0.72 | 0.81 | 56 | 6HI |
| 4 | 587 | 0.72 | 0.80 | 72 | 6HI |
| 5 | 437 | 0.71 | 0.82 | 62 | 6HI |
Interfaces
6 interfaces between chains.
- A–B · 4180 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 4146 Ų buried · 77 hydrogen bonds · protein-protein
- B–C · 1371 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1346 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3CD0 · Thermodynamic and structure guided design of statin hmg-CoA reductase inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- P04035 · AlphaFold monomer V2.0 prediction for 3-hydroxy-3-methylglutaryl- coenzyme a reductase… · a predicted model of the same protein · chain D 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 P04035
- Elsewhere: RCSB PDB 3CD0 · PDBe 3CD0 · UniProt P04035
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