MolNFT v1 · #32566 · protein
Crystal structure of human dipeptidyl peptidase IV (CD26) in complex with a reversed amide inhibitor
2BUB · Dipeptidyl peptidase 4: “Crystal structure of human dipeptidyl peptidase IV (CD26) in complex with a reversed amide inhibitor”. X-ray diffraction, 2 ligands (FPB, NAG), 20 pockets (best druggability 0.73). MolNFT v1 #32566 on…
- PDB
- 2BUB
- 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
- FPB, NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- FPB · N-({(2S)-1-[(3R)-3-amino-4-(2-fluorophenyl) butanoyl]pyrrolidin-2-yl}methyl)benzamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.73 | 0.97 | 16 | empty |
| 2 | 569 | 0.67 | 0.77 | 66 | FPB |
| 3 | 578 | 0.64 | 0.75 | 69 | FPB |
| 4 | 361 | 0.54 | 0.74 | 44 | empty |
| 5 | 128 | 0.54 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2317 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2BUB · Crystal Structure Of Human Dipeptidyl Peptidase IV (CD26) in Complex with a Reversed… · 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 2BUB · PDBe 2BUB · UniProt P27487
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