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Human dipeptidyl peptidase IV (DPP4) with piperidinone-constrained phenethylamine
Analyse Human dipeptidyl peptidase IV (DPP4) with piperidinone-constrained… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OQI
- Type
- protein
- Length
- 2,904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4 (dipeptidyl peptidase IV) (dpp IV) (T-cell activation antigen…
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- GGO
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidyl peptidase 4 (dipeptidyl peptidase IV) (dpp IV) (T-cell activation antigen CD26) (TP103) (adenosine deaminase complexing protein 2) (adabp) (EC 3.4.14.5) | protein | 726 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- GGO · (4R,5R)-5-amino-1-[2-(1,3-benzodioxol-5-yl)ethyl]-4-(2,4,5-trifluorophenyl)piperidin-2-one · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.75 | 0.98 | 22 | empty |
| 2 | 63 | 0.72 | 0.97 | 22 | empty |
| 3 | 681 | 0.69 | 0.77 | 80 | empty |
| 4 | 496 | 0.65 | 0.77 | 65 | empty |
| 5 | 491 | 0.65 | 0.77 | 70 | GGO |
Interfaces
2 interfaces between chains.
- C–D · 2326 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2307 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2OQI · Human Dipeptidyl Peptidase IV (DPP4) with Piperidi -constrained phenethylamine · the same entry in another collection · chain D against D, 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 2OQI · PDBe 2OQI · UniProt P27487
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