Research workbench
Human dipeptidyl peptidase IV in complex with 5-aminomethyl-6-(2,4- dichloro-phenyl)-2-(3,5-dimethoxy-phenyl)-pyrimidin-4-ylamine
Analyse Human dipeptidyl peptidase IV in complex with 5-aminomethyl-6-(2,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RWQ
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 5AP, NAG
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- 5AP · 5-(aminomethyl)-6-(2,4-dichlorophenyl)-2-(3,5-dimethoxyphenyl)pyrimidin-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
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.71 | 0.77 | 100 | 5AP |
| 2 | 805 | 0.70 | 0.76 | 99 | 5AP |
| 3 | 53 | 0.70 | 0.97 | 18 | empty |
| 4 | 334 | 0.59 | 0.77 | 47 | empty |
| 5 | 231 | 0.53 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2308 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1RWQ · Human Dipeptidyl peptidase IV in complex with 5-aminomethyl-6-(2,4-dichloro-phenyl)-2-(3,5… · 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 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 1RWQ · PDBe 1RWQ · UniProt P27487
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