MolNFT v1 · #96628 · protein
MMP13 in complex with a piperazine hydantoin ligand
4JPA · Collagenase 3: “MMP13 in complex with a piperazine hydantoin ligand”. X-ray diffraction, 4 ligands (AZ6, ZN, CA), 2 pockets (best druggability 0.72). MolNFT v1 #96628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JPA
- Type
- protein
- Length
- 331 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
- AZ6, ZN, CA, NA
- Pockets
- 2 · best druggability 0.72
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 | 165 | 24% helix, 18% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 24% helix, 19% strand | P45452 |
Ligands and binding sites
- AZ6 · 3-[({2-[4-({[(4S)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}sulfonyl)piperazin-1-yl]pyrimidin-5-yl}oxy)methyl]benzonitrile · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.72 | 0.76 | 84 | ZN, AZ6 |
| 2 | 131 | 0.47 | 0.78 | 21 | ZN, AZ6 |
Interfaces
1 interface between chains.
- A–B · 1258 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4JPA · Mmp13 in complex with a piperazine hydantoin ligand · 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 4JPA · PDBe 4JPA · UniProt P45452
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