MolNFT v1 · #50454 · protein
Structure of dppiv in complex with an inhibitor
2RIP · Dipeptidyl peptidase 4: “Structure of dppiv in complex with an inhibitor”. X-ray diffraction, 3 ligands (34Q, NAG, MAN), 7 pockets (best druggability 0.71). MolNFT v1 #50454 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2RIP
- Type
- protein
- Length
- 729 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 34Q, NAG, MAN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 729 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- 34Q · (3R,4R)-4-(pyrrolidin-1-ylcarbonyl)-1-(quinoxalin-2-ylcarbonyl)pyrrolidin-3-amine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.71 | 0.76 | 109 | 34Q |
| 2 | 172 | 0.48 | 0.77 | 31 | empty |
| 3 | 173 | 0.48 | 0.77 | 30 | empty |
| 4 | 102 | 0.46 | 0.79 | 17 | empty |
| 5 | 257 | 0.46 | 0.72 | 28 | empty |
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, 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 2RIP · PDBe 2RIP · UniProt P27487
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