Research workbench

Human DPP4 in complex with a ligand 34A

Analyse Human DPP4 in complex with a ligand 34A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T4B
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: 75N, NAG, NA
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	728	17% helix, 38% strand	P27487

Ligands and binding sites

75N · 2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-5-[(4-methylquinazolin-2-yl)methyl]-3H-imidazo[2,1-b]purin-4(5H)-one · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
NA · Sodium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.74	0.98	22	empty
2	687	0.69	0.76	89	75N
3	748	0.69	0.76	83	75N
4	243	0.53	0.76	33	empty
5	245	0.52	0.76	37	empty

Interfaces

1 interface between chains.

A–B · 2314 Å² buried · 45 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).

Compared structures

5T4B · Human DPP4 in complex with a ligand 34a · 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 5T4B · PDBe 5T4B · UniProt P27487

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