Research workbench
Crystal structure of human dipeptidyl peptidase IV (dppiv) complexed with cyanopyrrolidine (C5-pro-pro) inhibitor 21AC
Analyse Crystal structure of human dipeptidyl peptidase IV (dppiv) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G5P
- Type
- protein
- Length
- 1,452 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
- ADF
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- ADF · 4-{[(2R,5S)-5-{[(2S)-2-(aminomethyl)pyrrolidin-1-yl]carbonyl}pyrrolidin-2-yl]methoxy}-3-tert-butylbenzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.97 | 22 | empty |
| 2 | 704 | 0.69 | 0.76 | 92 | ADF |
| 3 | 642 | 0.68 | 0.77 | 75 | empty |
| 4 | 401 | 0.54 | 0.73 | 49 | empty |
| 5 | 224 | 0.52 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2315 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2G5P · Crystal structure of human dipeptidyl peptidase IV (DPPIV) complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · 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 P27487
- Elsewhere: RCSB PDB 2G5P · PDBe 2G5P · UniProt P27487
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