Research workbench
Crystal structure of ABAD/HSD10 with a bound inhibitor
Analyse Crystal structure of ABAD/HSD10 with a bound inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U7T
- Type
- protein
- Length
- 1,020 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase type II
- EC
- 1.1.1.35
- UniProt
- Q99714
- Ligands
- TDT, NAD
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-hydroxyacyl-CoA dehydrogenase type II (EC 1.1.1.35) | protein | 255 | 45% helix, 17% strand | Q99714 |
Ligands and binding sites
- TDT · 1-azepan-1-yl-2-phenyl-2-(4-thioxo-1,4-dihydro-pyrazolo[3,4-d]pyrimidin-5-yl)ethanone adduct · ligand · 3 copies · chains A, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.85 | 0.86 | 66 | empty |
| 2 | 425 | 0.73 | 0.83 | 50 | TDT |
| 3 | 426 | 0.73 | 0.83 | 52 | TDT |
| 4 | 422 | 0.72 | 0.83 | 51 | TDT |
| 5 | 416 | 0.69 | 0.81 | 47 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 1911 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1890 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1562 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1556 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1U7T · Crystal Structure of ABAD/HSD10 with a Bound Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q99714 · AlphaFold monomer V2.0 prediction for 3-hydroxyacyl-CoA dehydrogenase type-2 (Q99714) · 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 Q99714
- Elsewhere: RCSB PDB 1U7T · PDBe 1U7T · UniProt Q99714
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