MolNFT v1 · #85271 · protein
MMP13 in complex with a novel selective non zinc binding inhibitor CMPD22
4A7B · Collagenase 3: “MMP13 in complex with a novel selective non zinc binding inhibitor CMPD22”. X-ray diffraction, 6 ligands (HAE, 3W5, 3W4), 2 pockets (best druggability 0.74). MolNFT v1 #85271 on GenesisL1: 3D structure, binding sites…
- PDB
- 4A7B
- Type
- protein
- Length
- 335 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
- HAE, 3W5, 3W4, ZN, CA, NA
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 169 | 23% helix, 19% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 23% helix, 19% strand | P45452 |
Ligands and binding sites
- HAE · Acetohydroxamic acid · ligand · 2 copies · chains A, B
- 3W5 · N-[(3S)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide · ligand · chains A
- 3W4 · N-[(3R)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide · ligand · chains 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
- GOL · Glycerol · additive · 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 | 1118 | 0.74 | 0.77 | 117 | 3W5, HAE, GOL, ZN, 3W4 |
| 2 | 51 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1196 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4A7B · MMP13 in complex with a novel selective non zinc binding inhibitor CMPD22 · 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 4A7B · PDBe 4A7B · UniProt P45452
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