Research workbench
Rat dpp-IV with xanthine inhibitor 4
Analyse Rat dpp-IV with xanthine inhibitor 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GBI
- 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
- XIH
- Pockets
- 18 · best druggability 0.78
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 | 730 | 18% helix, 36% strand | P14740 |
Ligands and binding sites
- XIH · 2-({8-[(3R)-3-aminopiperidin-1-yl]-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl}methyl)benzonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.78 | 0.95 | 26 | empty |
| 2 | 567 | 0.68 | 0.78 | 66 | empty |
| 3 | 564 | 0.67 | 0.77 | 61 | XIH |
| 4 | 203 | 0.53 | 0.78 | 29 | empty |
| 5 | 207 | 0.51 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2199 Ų buried · 40 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 P14740
- Elsewhere: RCSB PDB 2GBI · PDBe 2GBI · UniProt P14740
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