Research workbench
Human dipeptidyl peptidase IV in complex with 1-(3,4-dimethoxy-phenyl) -3-M-tolyl-piperidine-4-ylamine
Analyse Human dipeptidyl peptidase IV in complex with 1-(3,4-dimethoxy-phenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JID
- Type
- protein
- Length
- 1,456 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
- GVB, NAG
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 19% helix, 36% strand | P27487 |
Ligands and binding sites
- GVB · (3R,4S)-1-(3,4-dimethoxyphenyl)-3-(3-methylphenyl)piperidin-4-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.70 | 0.76 | 88 | GVB |
| 2 | 518 | 0.66 | 0.77 | 61 | GVB |
| 3 | 542 | 0.61 | 0.74 | 60 | empty |
| 4 | 240 | 0.53 | 0.77 | 33 | empty |
| 5 | 241 | 0.52 | 0.76 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 2312 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2JID · Human Dipeptidyl peptidase IV in complex with 1-(3,4-Dimethoxy-phenyl)… · 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 2JID · PDBe 2JID · UniProt P27487
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