Research workbench
Crystal structure of human adamts-4 in complex with inhibitor 5- chloro-N-{[(4R)-2,5-dioxo-4-(1,3-thiazol-2-YL)IMIDAZOLIDIN-4- YL]METHYL}-1-benzofuran-2-carboxamide (compound 10)
Analyse Crystal structure of human adamts-4 in complex with inhibitor 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WKE
- Type
- protein
- Length
- 214 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A disintegrin and metalloproteinase with thrombospondin motifs 4
- EC
- 3.4.24.82
- UniProt
- O75173
- Ligands
- 3PU, CA, ZN
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A disintegrin and metalloproteinase with thrombospondin motifs 4 (EC 3.4.24.82) | protein | 214 | 36% helix, 15% strand | O75173 |
Ligands and binding sites
- 3PU · 5-chloro-N-{[(4R)-2,5-dioxo-4-(1,3-thiazol-2-yl)imidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.45 | 0.80 | 20 | EDO, 3PU |
| 2 | 63 | 0.31 | 0.75 | 14 | empty |
| 3 | 54 | 0.31 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4WKE · Crystal structure of human ADAMTS-4 in complex with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- O75173 · AlphaFold monomer V2.0 prediction for a disintegrin and metalloproteinase with… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O75173
- Elsewhere: RCSB PDB 4WKE · PDBe 4WKE · UniProt O75173
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