Research workbench
Rat dpp-IV with alkynyl cyanopyrrolidine #2
Analyse Rat dpp-IV with alkynyl cyanopyrrolidine #2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GBG
- Type
- protein
- Length
- 1,460 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
- P14740
- Ligands
- 1AD, SO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 730 | 19% helix, 36% strand | P14740 |
Ligands and binding sites
- 1AD · (1S)-2-[(2S,5R)-2-(aminomethyl)-5-prop-1-yn-1-ylpyrrolidin-1-yl]-1-cyclopentyl-2-oxoethanamine · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.79 | 0.96 | 26 | empty |
| 2 | 748 | 0.70 | 0.76 | 90 | empty |
| 3 | 341 | 0.60 | 0.77 | 44 | SO4 |
| 4 | 309 | 0.57 | 0.76 | 39 | SO4, 1AD |
| 5 | 207 | 0.52 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2184 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).
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 P14740
- Elsewhere: RCSB PDB 2GBG · PDBe 2GBG · UniProt P14740
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