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The structure of DPP4 in complex with vildagliptin analog

Analyse The structure of DPP4 in complex with vildagliptin analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B1O
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: C8S, NAG
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	728	18% helix, 38% strand	P27487

Ligands and binding sites

C8S · (2S)-2-amino-1-[(1S,3S,5S)-3-(aminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(1r,3R,5S,7S)-3,5-dihydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-one · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.75	0.98	24	empty
2	751	0.69	0.76	87	C8S
3	576	0.67	0.77	69	C8S
4	399	0.55	0.73	52	empty
5	278	0.54	0.76	34	empty

Interfaces

1 interface between chains.

A–B · 2319 Å² buried · 45 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 10 disulfide, 2 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

6B1O · The structure of DPP4 in complex with Vildagliptin Analog · 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 6B1O · PDBe 6B1O · UniProt P27487

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