MolNFT v1 · #75790 · protein
Crystal structure of human dpp-IV in complex withsa-(+)- METHYL2-(3- (aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl- 7-oxo-5H-PYRROLO[3,4- B]PYRIDIN-6(7H)-YL)ACETATE
3Q0T · Dipeptidyl peptidase 4: “Crystal structure of human dpp-IV in complex withsa-(+)- METHYL2-(3…”. X-ray diffraction, 2 ligands (LGE, NAG), 20 pockets (best druggability 0.73). MolNFT v1 #75790 on GenesisL1: 3D structure, binding sites…
- PDB
- 3Q0T
- 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
- LGE, NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- LGE · methyl [3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-7-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]acetate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 18 | empty |
| 2 | 675 | 0.68 | 0.76 | 81 | LGE |
| 3 | 506 | 0.65 | 0.77 | 65 | LGE |
| 4 | 205 | 0.52 | 0.77 | 31 | empty |
| 5 | 205 | 0.49 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2293 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
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 3Q0T · PDBe 3Q0T · UniProt P27487
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