MolNFT v1 · #47350 · protein
Mmp-9 active site mutant with barbiturate inhibitor
2OVX · Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda…: “Mmp-9 active site mutant with barbiturate inhibitor”. X-ray diffraction, 4 ligands (4MR, CA, ZN), 5 pockets (best druggability 0.61). MolNFT v1 #47350 on GenesisL1: 3D…
- PDB
- 2OVX
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda type IV collagenase) (92 kda…
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- 4MR, CA, ZN, CL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda type IV collagenase) (92 kda gelatinase) (gelatinase B) (gelb) (EC 3.4.24.35) | protein | 159 | 24% helix, 17% strand | P14780 |
Ligands and binding sites
- 4MR · 5-(4-phenoxyphenyl)-5-(4-pyrimidin-2-ylpiperazin-1-yl)pyrimidine-2,4,6(2H,3H)-trione · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 10 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.61 | 0.82 | 31 | ZN, 4MR |
| 2 | 181 | 0.58 | 0.81 | 25 | 4MR |
| 3 | 174 | 0.50 | 0.78 | 30 | CL |
| 4 | 64 | 0.49 | 0.85 | 19 | empty |
| 5 | 110 | 0.45 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 9 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 P14780
- Elsewhere: RCSB PDB 2OVX · PDBe 2OVX · UniProt P14780
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