MolNFT v1 · #79230 · protein
Crystal structure of human dpp-IV in complex with sa-(+)-3- (aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)- 2-methyl- 5H-PYRROLO[3,4-B]PYRIDIN-7(6H)-one
3SX4 · Dipeptidyl peptidase 4: “Crystal structure of human dpp-IV in complex with sa-(+)-3…”. X-ray diffraction, 2 ligands (KXA, NAG), 18 pockets (best druggability 0.75). MolNFT v1 #79230 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3SX4
- Type
- protein
- Length
- 1,453 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
- KXA, NAG
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- KXA · 3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.75 | 0.97 | 22 | empty |
| 2 | 511 | 0.66 | 0.77 | 68 | KXA |
| 3 | 475 | 0.65 | 0.77 | 62 | KXA |
| 4 | 342 | 0.57 | 0.76 | 49 | empty |
| 5 | 400 | 0.56 | 0.74 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 2213 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 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 3SX4 · PDBe 3SX4 · UniProt P27487
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