MolNFT v1 · #98171 · protein
Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1
4L19 · Collagenase 3: “Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1”. X-ray diffraction, 3 ligands (1UA, ZN, CA), 2 pockets (best druggability 0.71). MolNFT v1 #98171 on GenesisL1: 3D structure, binding sites…
- PDB
- 4L19
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- 1UA, ZN, CA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 24% helix, 19% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 170 | 24% helix, 18% strand | P45452 |
Ligands and binding sites
- 1UA · 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one · ligand · 3 copies · chains A, B
- ZN · Zinc ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.71 | 0.76 | 79 | FMT, 1UA, GOL |
| 2 | 277 | 0.58 | 0.78 | 40 | FMT, 1UA |
Interfaces
1 interface between chains.
- A–B · 1233 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4L19 · Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1 · the same entry in another collection · chain A against A, TM-score 1.00
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 P45452
- Elsewhere: RCSB PDB 4L19 · PDBe 4L19 · UniProt P45452
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