Research workbench
Crystal structure of human dipeptidyl peptidase IV (dpp IV) complexed with abt-341, a cyclohexene-constrained phenethylamine inhibitor
Analyse Crystal structure of human dipeptidyl peptidase IV (dpp IV) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I78
- Type
- protein
- Length
- 2,904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- KIQ
- Pockets
- 20 · 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, C, D | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 726 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- KIQ · (1S,6R)-3-{[3-(trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]carbonyl}-6-(2,4,5-trifluorophenyl)cyclohex-3-en-1-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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.75 | 0.97 | 22 | empty |
| 2 | 62 | 0.73 | 0.98 | 18 | empty |
| 3 | 712 | 0.70 | 0.77 | 83 | KIQ |
| 4 | 759 | 0.70 | 0.76 | 88 | empty |
| 5 | 569 | 0.68 | 0.77 | 78 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2314 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2300 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2I78 · Crystal structure of human dipeptidyl peptidase IV (DPP IV) complexed with ABT-341, a… · 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 B 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 2I78 · PDBe 2I78 · UniProt P27487
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.