MolNFT v1 · #140334 · protein
Crystal structure of human DPP4 in complex with INHIBITOR1
5Y7K · Dipeptidyl peptidase 4: “Crystal structure of human DPP4 in complex with INHIBITOR1”. X-ray diffraction, 1 ligand (8VU), 20 pockets (best druggability 0.77). MolNFT v1 #140334 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5Y7K
- Type
- protein
- Length
- 2,907 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
- 8VU
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 725 | 18% helix, 37% strand | P27487 |
| B, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 37% strand | P27487 |
| C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- 8VU · (R)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl)piperazine-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 | 89 | 0.77 | 0.98 | 24 | empty |
| 2 | 51 | 0.70 | 0.98 | 16 | empty |
| 3 | 702 | 0.68 | 0.76 | 92 | 8VU |
| 4 | 658 | 0.68 | 0.76 | 80 | 8VU |
| 5 | 596 | 0.68 | 0.77 | 80 | 8VU |
Interfaces
4 interfaces between chains.
- A–B · 2308 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2280 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 337 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 18 Ų buried · 0 hydrogen bonds · 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 5Y7K · PDBe 5Y7K · UniProt P27487
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