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Crystal structure analysis of dppiv inhibitor
Analyse Crystal structure analysis of dppiv inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EIO
- Type
- protein
- Length
- 1,454 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
- AJH, NAG, MAN
- Pockets
- 17 · best druggability 0.73
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 | 726 | 17% helix, 37% strand | P27487 |
| B | Dipeptidyl peptidase 4 soluble form (EC 3.4.14.5) | protein | 728 | 17% helix, 38% strand | P27487 |
Ligands and binding sites
- AJH · 4-({4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-1,4-diazepan-1-yl}carbonyl)benzoic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 22 | empty |
| 2 | 867 | 0.71 | 0.76 | 99 | AJH |
| 3 | 536 | 0.65 | 0.76 | 64 | AJH |
| 4 | 457 | 0.57 | 0.73 | 51 | empty |
| 5 | 196 | 0.51 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2318 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
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 3EIO · PDBe 3EIO · UniProt P27487
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