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Crystal structure of human dipeptidyl peptidase IV (dppiv) complex with cyclic hydrazine derivatives
Analyse Crystal structure of human dipeptidyl peptidase IV (dppiv) complex with cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OLE
- Type
- protein
- Length
- 1,454 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
- KR2
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 19% helix, 38% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- KR2 · (2R)-4-(2-benzoyl-1,2-diazepan-1-yl)-4-oxo-1-(2,4,5-trifluorophenyl)butan-2-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.69 | 0.76 | 86 | KR2 |
| 2 | 632 | 0.68 | 0.76 | 78 | KR2 |
| 3 | 444 | 0.55 | 0.73 | 51 | empty |
| 4 | 221 | 0.50 | 0.76 | 35 | empty |
| 5 | 219 | 0.49 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2310 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2OLE · Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Cyclic Hydrazine… · 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 2OLE · PDBe 2OLE · UniProt P27487
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