MolNFT v1 · #140333 · protein
Crystal structure of human DPP4 in complex with INHIBITOR2
5Y7J · Dipeptidyl peptidase 4: “Crystal structure of human DPP4 in complex with INHIBITOR2”. X-ray diffraction, 1 ligand (8OL), 20 pockets (best druggability 0.71). MolNFT v1 #140333 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5Y7J
- Type
- protein
- Length
- 2,905 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
- 8OL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 725 | 17% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 36% strand | P27487 |
| D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- 8OL · (S)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl)piperazin-2-one · ligand · 4 copies · chains A, B, C, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.71 | 0.98 | 16 | empty |
| 2 | 882 | 0.71 | 0.76 | 98 | empty |
| 3 | 51 | 0.71 | 0.98 | 16 | empty |
| 4 | 731 | 0.69 | 0.76 | 89 | 8OL |
| 5 | 700 | 0.69 | 0.76 | 91 | 8OL |
Interfaces
4 interfaces between chains.
- A–B · 2295 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2294 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
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 5Y7J · PDBe 5Y7J · UniProt P27487
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