MolNFT v1 · #103684 · protein
Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor omarigliptin (mk-3102)
4PNZ · Dipeptidyl peptidase 4: “Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor omarigliptin (mk-3102)”. X-ray diffraction, 3 ligands (2VH, NAG, NA), 17 pockets (best druggability 0.76). MolNFT v1 #103684 on…
- PDB
- 4PNZ
- Type
- protein
- Length
- 1,455 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
- 2VH, NAG, NA
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 38% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- 2VH · (2R,3S,5R)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl]-2-(2,4,5-trifluorophenyl)tetrahydro-2H-pyran-3-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.76 | 0.98 | 22 | empty |
| 2 | 717 | 0.70 | 0.77 | 92 | 2VH |
| 3 | 753 | 0.70 | 0.76 | 91 | 2VH |
| 4 | 269 | 0.55 | 0.77 | 34 | empty |
| 5 | 385 | 0.53 | 0.72 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2310 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 4PNZ · Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor Omarigliptin… · 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 4PNZ · PDBe 4PNZ · UniProt P27487
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