MolNFT v1 · #49296 · protein

Dipepdyl peptidase IV in complex with inhibitor pzf

2QJR · Dipeptidyl peptidase 4 membrane form: “Dipepdyl peptidase IV in complex with inhibitor pzf”. X-ray diffraction, 4 ligands (LGU, PZF, NAG), 17 pockets (best druggability 0.72). MolNFT v1 #49296 on GenesisL1: 3D structure, binding…

PDB: 2QJR
Type: protein
Length: 1,456 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 4 membrane form
UniProt: P27487
Ligands: LGU, PZF, NAG, MAN
Pockets: 17 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 membrane form	protein	728	18% helix, 38% strand	P27487

Ligands and binding sites

LGU · alpha-L-gulopyranuronic acid · ligand · 2 copies
PZF · (3R,4S)-1-[6-(6-methoxypyridin-3-yl)pyrimidin-4-yl]-4-(2,4,5-trifluorophenyl)pyrrolidin-3-amine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.72	0.98	16	empty
2	718	0.69	0.76	84	PZF
3	583	0.67	0.77	79	PZF
4	434	0.56	0.73	53	empty
5	268	0.56	0.77	46	empty

Interfaces

1 interface between chains.

A–B · 2292 Å² buried · 47 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

2QJR · dipepdyl peptidase IV in complex with inhibitor PZF · 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 2QJR · PDBe 2QJR · UniProt P27487

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