Research workbench
Human dipeptidyl peptidase IV/CD26 in complex with a 4-aryl cyclohexylalanine inhibitor
Analyse Human dipeptidyl peptidase IV/CD26 in complex with a 4-aryl cyclohexylalanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QTB
- Type
- protein
- Length
- 1,456 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
- 474, NAG, NDG, NA
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- 474 · (2S,3S)-3-amino-4-(3,3-difluoropyrrolidin-1-yl)-N,N-dimethyl-4-oxo-2-(trans-4-[1,2,4]triazolo[1,5-a]pyridin-6-ylcyclohexyl)butanamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.75 | 0.98 | 22 | empty |
| 2 | 757 | 0.69 | 0.76 | 91 | 474 |
| 3 | 694 | 0.68 | 0.76 | 88 | 474 |
| 4 | 382 | 0.53 | 0.73 | 46 | empty |
| 5 | 237 | 0.52 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2301 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 2QTB · Human dipeptidyl peptidase iv/cd26 in complex with a 4-aryl cyclohexylalanine 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 2QTB · PDBe 2QTB · UniProt P27487
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