Research workbench
Crystal structure of human DPP4 in complex with a noval heterocyclic DPP4 inhibitor
Analyse Crystal structure of human DPP4 in complex with a noval heterocyclic DPP4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A5S
- Type
- protein
- Length
- 1,460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4 soluble form
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- N7F, NAG, MAN, SO4
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 soluble form (EC 3.4.14.5) | protein | 727 | 17% helix, 38% strand | P27487 |
| B | Dipeptidyl peptidase 4 soluble form (EC 3.4.14.5) | protein | 733 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- N7F · 6-[(3S)-3-aminopiperidin-1-yl]-5-benzyl-4-oxo-3-(quinolin-4-ylmethyl)-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidine-7-carbonitrile · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- SO4 · Sulfate ion · ion · 6 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.98 | 16 | empty |
| 2 | 721 | 0.70 | 0.77 | 82 | N7F |
| 3 | 546 | 0.66 | 0.77 | 63 | N7F |
| 4 | 397 | 0.57 | 0.75 | 47 | empty |
| 5 | 227 | 0.53 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2343 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 4A5S · Crystal structure of human DPP4 in complex with a noval heterocyclic DPP4 inhibitor · 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 4A5S · PDBe 4A5S · UniProt P27487
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