MolNFT v1 · #31101 · protein
X-ray structure of novel biaryl-based dipeptidyl peptidase IV inhibitor
2AJL · Dipeptidyl peptidase 4: “X-ray structure of novel biaryl-based dipeptidyl peptidase IV inhibitor”. X-ray diffraction, 2 ligands (JNH, NAG), 18 pockets (best druggability 0.70). MolNFT v1 #31101 on GenesisL1: 3D structure, binding…
- PDB
- 2AJL
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- JNH, NAG
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 37% strand | P27487 |
| J | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- JNH · 1-[2-(S)-amino-3-biphenyl-4-yl-propionyl]-pyrrolidine-2-(S)-carbonitrile · ligand · 2 copies · chains I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.70 | 0.97 | 17 | empty |
| 2 | 629 | 0.67 | 0.76 | 77 | JNH |
| 3 | 495 | 0.65 | 0.77 | 65 | JNH |
| 4 | 480 | 0.57 | 0.73 | 54 | empty |
| 5 | 400 | 0.54 | 0.73 | 52 | empty |
Interfaces
1 interface between chains.
- I–J · 2264 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2AJL · X-ray Structure of Novel Biaryl-Based Dipeptidyl peptidase IV inhibitor · the same entry in another collection · chain I against I, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · chain I 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 2AJL · PDBe 2AJL · UniProt P27487
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