MolNFT v1 · #59647 · protein
Human dipeptidyl peptidase IV/CD26 in complex with a fluoroolefin inhibitor
3C45 · Dipeptidyl peptidase 4 soluble form: “Human dipeptidyl peptidase IV/CD26 in complex with a fluoroolefin inhibitor”. X-ray diffraction, 3 ligands (317, NAG, NA), 16 pockets (best druggability 0.75). MolNFT v1 #59647 on GenesisL1: 3D…
- PDB
- 3C45
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4 soluble form
- UniProt
- P27487
- Ligands
- 317, NAG, NA
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 soluble form | protein | 728 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- 317 · (2S,3S)-3-{3-[2-chloro-4-(methylsulfonyl)phenyl]-1,2,4-oxadiazol-5-yl}-1-cyclopentylidene-4-cyclopropyl-1-fluorobutan-2-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.75 | 0.98 | 22 | empty |
| 2 | 781 | 0.69 | 0.76 | 96 | 317 |
| 3 | 702 | 0.69 | 0.77 | 88 | 317 |
| 4 | 284 | 0.55 | 0.76 | 43 | empty |
| 5 | 229 | 0.53 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2308 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 3C45 · Human dipeptidyl peptidase IV/CD26 in complex with a fluoroolefin 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 3C45 · PDBe 3C45 · UniProt P27487
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