MolNFT v1 · #40198 · protein
Human dipeptidyl peptidase 4 in complex with a diazepan-2-one inhibitor
2IIV · Dipeptidyl peptidase 4 soluble form: “Human dipeptidyl peptidase 4 in complex with a diazepan-2-one inhibitor”. X-ray diffraction, 2 ligands (565, NAG), 16 pockets (best druggability 0.73). MolNFT v1 #40198 on GenesisL1: 3D…
- PDB
- 2IIV
- Type
- protein
- Length
- 1,456 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
- 565, NAG
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 soluble form (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- 565 · (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-methyl-1,4-diazepan-2-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.73 | 0.98 | 16 | empty |
| 2 | 763 | 0.69 | 0.76 | 89 | 565 |
| 3 | 659 | 0.68 | 0.77 | 83 | 565 |
| 4 | 221 | 0.52 | 0.76 | 32 | empty |
| 5 | 225 | 0.51 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2302 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 2IIV · Human dipeptidyl peptidase 4 in complex with a diazepan-2-one 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 2IIV · PDBe 2IIV · UniProt P27487
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