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Crystal structure of dpp-IV with compound C2
Analyse Crystal structure of dpp-IV with compound C2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DSZ
- Type
- protein
- Length
- 1,448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- DC3
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 724 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- DC3 · (2R)-4-[4-(3-methylphenyl)-1H-1,2,3-triazol-1-yl]-1-(2,4,5-trifluorophenyl)butan-2-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.73 | 0.99 | 13 | empty |
| 2 | 785 | 0.69 | 0.76 | 90 | DC3 |
| 3 | 533 | 0.65 | 0.77 | 71 | DC3 |
| 4 | 451 | 0.57 | 0.74 | 51 | empty |
| 5 | 244 | 0.55 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2249 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
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 4DSZ · PDBe 4DSZ · UniProt P27487
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