MolNFT v1 · #76056 · protein
A B-aminoacyl containing thiazolidine derivative and dppiv complex
3Q8W · Dipeptidyl peptidase 4: “A B-aminoacyl containing thiazolidine derivative and dppiv complex”. X-ray diffraction, 1 ligand (AZV), 16 pockets (best druggability 0.75). MolNFT v1 #76056 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3Q8W
- Type
- protein
- Length
- 1,452 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
- AZV
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 33% strand | P27487 |
Ligands and binding sites
- AZV · N-(4-{[({(2R)-3-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-1,3-thiazolidin-2-yl}carbonyl)amino]methyl}phenyl)-D-valine · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.75 | 0.97 | 24 | empty |
| 2 | 806 | 0.72 | 0.77 | 103 | AZV |
| 3 | 749 | 0.70 | 0.76 | 88 | AZV |
| 4 | 175 | 0.58 | 0.81 | 20 | empty |
| 5 | 175 | 0.55 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2286 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3Q8W · A b-aminoacyl containing thiazolidine derivative and DPPIV complex · the same entry in another collection · chain B against B, 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 0.99
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 3Q8W · PDBe 3Q8W · UniProt P27487
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