MolNFT v1 · #44511 · protein
NMR structure of an inhibitor bound dengue NS3 protease
2M9P · Serine protease subunit NS2B, serine protease NS3: “NMR structure of an inhibitor bound dengue NS3 protease”. Solution nmr, 2 ligands (BEZ, M9P), 3 pockets (best druggability 0.51). MolNFT v1 #44511 on GenesisL1: 3D structure…
- PDB
- 2M9P
- Type
- protein
- Length
- 243 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease subunit NS2B, serine protease NS3; Serine protease inhibitor
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- Ligands
- BEZ, M9P
- Pockets
- 3 · best druggability 0.51
Structure
solution nmr · 2 distinct chains · 0% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease subunit NS2B, serine protease NS3 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 240 | 0% helix, 42% strand | — |
| B | Serine protease inhibitor | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains A, B
- M9P · Amino{[(4s,5s)-4-amino-6,6,6-trifluoro-5-hydroxyhexyl]amino}methaniminium · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.51 | 0.81 | 32 | M9P |
| 2 | 118 | 0.43 | 0.76 | 20 | empty |
| 3 | 56 | 0.43 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2M9P · NMR structure of an inhibitor bound dengue NS3 protease · 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
- Elsewhere: RCSB PDB 2M9P · PDBe 2M9P
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