MolNFT v1 · #55372 · protein
MMP13 in complex with a novel selective non zinc binding inhibitor
2YIG · Collagenase 3: “MMP13 in complex with a novel selective non zinc binding inhibitor”. X-ray diffraction, 4 ligands (5EL, ZN, CA), 1 pocket (best druggability 0.74). MolNFT v1 #55372 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YIG
- Type
- protein
- Length
- 333 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
- 5EL, ZN, CA, NA
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 167 | 24% helix, 19% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 24% helix, 19% strand | P45452 |
Ligands and binding sites
- 5EL · 4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)-N-(pyridin-4-ylmethyl)benzamide · 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 · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.74 | 0.77 | 113 | 5EL, ZN, NA |
Interfaces
1 interface between chains.
- A–B · 1276 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2YIG · MMP13 in complex with a novel selective non zinc binding inhibitor · 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 2YIG · PDBe 2YIG · UniProt P45452
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