MolNFT v1 · #46637 · protein
Crystal structure of human dipeptidyl peptidase IV (dppiv) with pyrrolidine-constrained phenethylamine 29G
2OAG · Dipeptidyl peptidase 4: “Crystal structure of human dipeptidyl peptidase IV (dppiv) with pyrrolidine-constrained phenethylamine 29G”. X-ray diffraction, 1 ligand (DLI), 20 pockets (best druggability 0.75). MolNFT v1 #46637 on…
- PDB
- 2OAG
- Type
- protein
- Length
- 2,904 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
- DLI
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- DLI · (3R,4S)-1-{6-[3-(methylsulfonyl)phenyl]pyrimidin-4-yl}-4-(2,4,5-trifluorophenyl)pyrrolidin-3-amine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.75 | 0.98 | 23 | empty |
| 2 | 78 | 0.75 | 0.97 | 22 | empty |
| 3 | 680 | 0.69 | 0.77 | 85 | empty |
| 4 | 684 | 0.68 | 0.76 | 90 | DLI |
| 5 | 534 | 0.66 | 0.77 | 64 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2301 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2293 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2OAG · Crystal structure of human dipeptidyl peptidase IV (DPPIV) with pyrrolidine-constrained… · the same entry in another collection · chain D against D, 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 2OAG · PDBe 2OAG · UniProt P27487
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