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
- 3CD5
- Type
- protein
- Length
- 1,684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxy-3-methylglutaryl-coenzyme a reductase
- EC
- 1.1.1.34
- UniProt
- P04035
- Ligands
- 7HI, SO4
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.34) | protein | 425 | 43% helix, 22% strand | P04035 |
| C | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.34) | protein | 418 | 41% helix, 22% strand | P04035 |
| D | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.34) | protein | 416 | 42% helix, 22% strand | P04035 |
Ligands and binding sites
- 7HI · (3R,5R)-7-[3-(biphenyl-4-ylcarbamoyl)-2-ethyl-5,6,7,8-tetrahydrocyclohepta[b]pyrrol-1(4H)-yl]-3,5-dihydroxyheptanoic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.79 | 0.85 | 73 | 7HI, SO4 |
| 2 | 507 | 0.78 | 0.85 | 66 | SO4, 7HI |
| 3 | 438 | 0.78 | 0.86 | 66 | SO4, 7HI |
| 4 | 491 | 0.75 | 0.84 | 62 | SO4, 7HI |
| 5 | 719 | 0.75 | 0.80 | 68 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4541 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 4506 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 1351 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1350 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 697 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3CD5 · 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
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 3CD5 · PDBe 3CD5 · UniProt P04035
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