Research workbench
Crystal structure of human ACC2 bc domain in complex with nd-646, the primary amide of nd-630
Analyse Crystal structure of human ACC2 bc domain in complex with nd-646, the primary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KKN
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA carboxylase 2
- EC
- 6.4.1.2, 6.3.4.14
- UniProt
- O00763
- Ligands
- 6U3
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Acetyl-CoA carboxylase 2 (EC 6.4.1.2, 6.3.4.14) | protein | 482 | 36% helix, 22% strand | O00763 |
| C | Acetyl-CoA carboxylase 2 (EC 6.4.1.2, 6.3.4.14) | protein | 470 | 37% helix, 22% strand | O00763 |
Ligands and binding sites
- 6U3 · 2-[1-[(2~{R})-2-(2-methoxyphenyl)-2-(oxan-4-yloxy) ethyl]-5-methyl-6-(1,3-oxazol-2-yl)-2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-3-yl]-2-methyl-propanamide · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.74 | 0.81 | 70 | empty |
| 2 | 457 | 0.69 | 0.80 | 60 | empty |
| 3 | 321 | 0.64 | 0.80 | 45 | empty |
| 4 | 338 | 0.64 | 0.79 | 42 | 6U3 |
| 5 | 328 | 0.62 | 0.78 | 32 | 6U3 |
Interfaces
1 interface between chains.
- B–C · 672 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5KKN · Crystal structure of human ACC2 BC domain in complex with ND-646, the primary amide of… · the same entry in another collection · chain B against B, TM-score 1.00
- O00763 · AlphaFold monomer V2.0 prediction for acetyl-CoA carboxylase 2 (O00763) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 O00763
- Elsewhere: RCSB PDB 5KKN · PDBe 5KKN · UniProt O00763
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