MolNFT v1 · #102991 · protein
Crystal structure of KAPOSI'S sarcoma-associated herpesvirus (kshv) protease in complex with a dimer disruptor
4P2T · Kshv protease: “Crystal structure of KAPOSI'S sarcoma-associated herpesvirus (kshv) protease in complex with a dimer disruptor”. X-ray diffraction, 1 ligand (24Q), 3 pockets (best druggability 0.75). MolNFT v1 #102991 on GenesisL1…
- PDB
- 4P2T
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kshv protease
- UniProt
- O36607
- Ligands
- 24Q
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kshv protease | protein | 192 | 31% helix, 26% strand | O36607 |
| B | Kshv protease | protein | 190 | 32% helix, 28% strand | O36607 |
Ligands and binding sites
- 24Q · 6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide · ligand · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
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 | 952 | 0.75 | 0.78 | 71 | empty |
| 2 | 181 | 0.55 | 0.79 | 18 | 24Q |
| 3 | 151 | 0.46 | 0.75 | 19 | 24Q |
Interfaces
1 interface between chains.
- A–B · 828 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4P2T · Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex… · 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 O36607
- Elsewhere: RCSB PDB 4P2T · PDBe 4P2T · UniProt O36607
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