Research workbench
Human dipeptidyl peptidase IV (DPP4) with piperidine-constrained phenethylamine
Analyse Human dipeptidyl peptidase IV (DPP4) with piperidine-constrained phenethylamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OQV
- Type
- protein
- Length
- 1,452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4 (dipeptidyl peptidase IV) (dpp IV)
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- MA9
- Pockets
- 14 · 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 | Dipeptidyl peptidase 4 (dipeptidyl peptidase IV) (dpp IV) (EC 3.4.14.5) | protein | 726 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- MA9 · (3R,4R)-1-{6-[3-(methylsulfonyl)phenyl]pyrimidin-4-yl}-4-(2,4,5-trifluorophenyl)piperidin-3-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.75 | 0.98 | 22 | empty |
| 2 | 676 | 0.69 | 0.77 | 86 | empty |
| 3 | 497 | 0.64 | 0.76 | 67 | MA9 |
| 4 | 361 | 0.54 | 0.74 | 51 | empty |
| 5 | 256 | 0.54 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2320 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2OQV · Human Dipeptidyl Peptidase IV (DPP4) with piperidine-constrained phenethylamine · the same entry in another collection · chain A against A, 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 2OQV · PDBe 2OQV · UniProt P27487
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