MolNFT v1 · #136553 · protein
Matrix metalloproteinase-13 complexed with selective inhibitor compound 10D
5UWN · Collagenase 3: “Matrix metalloproteinase-13 complexed with selective inhibitor compound 10D”. X-ray diffraction, 4 ligands (8O7, ZN, CA), 9 pockets (best druggability 0.74). MolNFT v1 #136553 on GenesisL1: 3D structure, binding…
- PDB
- 5UWN
- Type
- protein
- Length
- 829 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- 8O7, ZN, CA, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 161 | 25% helix, 17% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 170 | 23% helix, 18% strand | P45452 |
| C | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 23% helix, 17% strand | P45452 |
| D | Collagenase 3 (EC 3.4.24.-) | protein | 165 | 24% helix, 18% strand | P45452 |
| E | Collagenase 3 (EC 3.4.24.-) | protein | 167 | 24% helix, 18% strand | P45452 |
Ligands and binding sites
- 8O7 · N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonamide · ligand · 5 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.74 | 0.77 | 112 | ZN, 8O7 |
| 2 | 441 | 0.74 | 0.84 | 57 | empty |
| 3 | 344 | 0.74 | 0.85 | 48 | 8O7 |
| 4 | 470 | 0.65 | 0.78 | 59 | 8O7, CA, SO4 |
| 5 | 303 | 0.58 | 0.77 | 32 | empty |
Interfaces
7 interfaces between chains.
- D–E · 772 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 756 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 741 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 276 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 262 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UWN · Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d · 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 5UWN · PDBe 5UWN · UniProt P45452
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