MolNFT v1 · #69056 · protein
Crystal structure of human mmp-13 complexed with a (pyridin-4-yl)-2H- tetrazole compound
3KEK · Collagenase 3: “Crystal structure of human mmp-13 complexed with a (pyridin-4-yl)-2H- tetrazole compound”. X-ray diffraction, 3 ligands (3EK, CA, ZN), 3 pockets (best druggability 0.64). MolNFT v1 #69056 on GenesisL1: 3D structure…
- PDB
- 3KEK
- Type
- protein
- Length
- 322 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
- 3EK, CA, ZN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 164 | 24% helix, 17% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 158 | 25% helix, 17% strand | P45452 |
Ligands and binding sites
- 3EK · trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.64 | 0.80 | 43 | 3EK |
| 2 | 243 | 0.61 | 0.81 | 37 | 3EK |
| 3 | 82 | 0.34 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 197 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KEK · Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound · 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 3KEK · PDBe 3KEK · UniProt P45452
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