Research workbench
ADAMTS1 in complex with a novel N-hydroxyformamide inhibitors
Analyse ADAMTS1 in complex with a novel N-hydroxyformamide inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q2G
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A disintegrin and metalloproteinase with thrombospondin motifs 1
- EC
- 3.4.24.-
- UniProt
- Q9UHI8
- Ligands
- QGF, NI, CD, ZN, MG, NA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A disintegrin and metalloproteinase with thrombospondin motifs 1 (EC 3.4.24.-) | protein | 282 | 32% helix, 18% strand | Q9UHI8 |
| B | A disintegrin and metalloproteinase with thrombospondin motifs 1 (EC 3.4.24.-) | protein | 282 | 31% helix, 18% strand | Q9UHI8 |
Ligands and binding sites
- QGF · N-[(2S,4S)-1-({4-[(2,4-dichlorobenzyl)oxy]piperidin-1-yl}sulfonyl)-4-(5-fluoropyrimidin-2-yl)-2-methylpentan-2-yl]-N-hydroxyformamide · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 14 copies · chains A, B
- CD · Cadmium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.74 | 0.82 | 58 | QGF, ZN, NI |
| 2 | 542 | 0.74 | 0.82 | 54 | QGF, ZN, MG |
| 3 | 384 | 0.67 | 0.80 | 47 | CD, NI |
| 4 | 345 | 0.63 | 0.79 | 45 | NI |
Interfaces
1 interface between chains.
- A–B · 992 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 3Q2G · Adamts1 in complex with a novel N-hydroxyformamide inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UHI8 · AlphaFold monomer V2.0 prediction for a disintegrin and metalloproteinase with… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9UHI8
- Elsewhere: RCSB PDB 3Q2G · PDBe 3Q2G · UniProt Q9UHI8
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