MolNFT v1 · #74198 · protein
Crystal structure of human DPP4 bound to tak-294
3OPM · Dipeptidyl peptidase 4: “Crystal structure of human DPP4 bound to tak-294”. X-ray diffraction, 2 ligands (LUI, NAG), 20 pockets (best druggability 0.70). MolNFT v1 #74198 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OPM
- Type
- protein
- Length
- 2,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- LUI, NAG
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 17% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 733 | 17% helix, 37% strand | P27487 |
| C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 725 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- LUI · 2-{[3-(aminomethyl)-2-(2-methylpropyl)-1-oxo-4-phenyl-1,2-dihydroisoquinolin-6-yl]oxy}acetamide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.70 | 0.74 | 143 | LUI |
| 2 | 698 | 0.69 | 0.77 | 87 | LUI |
| 3 | 710 | 0.69 | 0.77 | 87 | LUI |
| 4 | 628 | 0.68 | 0.77 | 75 | LUI |
| 5 | 123 | 0.58 | 0.83 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2331 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2324 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 180 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
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 3OPM · PDBe 3OPM · UniProt P27487
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