MolNFT v1 · #27017 · protein
Human dipeptidyl peptidase IV in complex with a beta amino acid inhibitor
1X70: “Human dipeptidyl peptidase IV in complex with a beta amino acid inhibitor”. X-ray diffraction, 4 ligands (715, NAG, NDG), 19 pockets (best druggability 0.74). MolNFT v1 #27017 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1X70
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 715, NAG, NDG, NA
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 728 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- 715 · (2R)-4-oxo-4-[3-(trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-1-(2,4,5-trifluorophenyl)butan-2-A mine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 22 | empty |
| 2 | 671 | 0.69 | 0.77 | 90 | 715 |
| 3 | 663 | 0.68 | 0.76 | 79 | 715 |
| 4 | 226 | 0.52 | 0.76 | 34 | empty |
| 5 | 242 | 0.52 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2287 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 1X70 · Human dipeptidyl peptidase IV in complex with a beta amino acid inhibitor · 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 1X70 · PDBe 1X70 · UniProt P27487
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