MolNFT v1 · #59915 · protein
Crystal structure of human DPP4 in complex with a benzimidazole derivative
3CCB · Dipeptidyl peptidase 4: “Crystal structure of human DPP4 in complex with a benzimidazole derivative”. X-ray diffraction, 2 ligands (B2Y, NAG), 20 pockets (best druggability 0.69). MolNFT v1 #59915 on GenesisL1: 3D structure, binding…
- PDB
- 3CCB
- Type
- protein
- Length
- 2,901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- B2Y, NAG
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 724 | 18% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 729 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- B2Y · 1-biphenyl-2-ylmethanamine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, D
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 | 721 | 0.69 | 0.76 | 86 | B2Y |
| 2 | 713 | 0.68 | 0.76 | 92 | B2Y |
| 3 | 663 | 0.68 | 0.76 | 82 | B2Y |
| 4 | 541 | 0.66 | 0.77 | 69 | B2Y |
| 5 | 556 | 0.61 | 0.74 | 68 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2316 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2304 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 3CCB · Crystal Structure of Human DPP4 in complex with a benzimidazole derivative · 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 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 3CCB · PDBe 3CCB · UniProt P27487
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