Research workbench
Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor
Analyse Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PV7
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.24
- Source
- Homo sapiens
- Molecule
- Dipeptidyl peptidase 4 soluble form
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- CJP
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · resolution 3.24 · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 soluble form (EC 3.4.14.5) | protein | 727 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- CJP · 1-[2-(2,4-dichlorophenyl)-1-(methylsulfonyl)-1H-indol-3-yl]methanamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.66 | 0.77 | 68 | CJP |
| 2 | 504 | 0.66 | 0.77 | 62 | CJP |
| 3 | 235 | 0.54 | 0.77 | 24 | empty |
| 4 | 212 | 0.53 | 0.77 | 31 | empty |
| 5 | 365 | 0.53 | 0.73 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2303 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4PV7 · Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · chain B 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 P27487
- Elsewhere: RCSB PDB 4PV7 · PDBe 4PV7 · UniProt P27487
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