MolNFT v1 · #3865 · protein
Crystal structure of MMP3 complexed with a thiazepine based inhibitor.
1D5J · Stromelysin-1: “Crystal structure of MMP3 complexed with a thiazepine based inhibitor.”. X-ray diffraction, 3 ligands (MM3, CA, ZN), 4 pockets (best druggability 0.71). MolNFT v1 #3865 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1D5J
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromelysin-1
- EC
- 3.4.24.17
- UniProt
- P08254
- Ligands
- MM3, CA, ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stromelysin-1 (EC 3.4.24.17) | protein | 169 | 24% helix, 18% strand | P08254 |
| B | Stromelysin-1 (EC 3.4.24.17) | protein | 173 | 22% helix, 16% strand | P08254 |
Ligands and binding sites
- MM3 · N-hydroxy-4-[(4-methoxylphenyl)sulfonyl]-2,2-dimethyl-hexahydro-1,4-thiazepine-3(S)-carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.71 | 0.82 | 45 | empty |
| 2 | 212 | 0.57 | 0.79 | 32 | ZN, MM3 |
| 3 | 146 | 0.47 | 0.77 | 31 | ZN, MM3 |
| 4 | 53 | 0.33 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 P08254
- Elsewhere: RCSB PDB 1D5J · PDBe 1D5J · UniProt P08254
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