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Crystal structure of human dpp-IV in complex with anagliptin

Analyse Crystal structure of human dpp-IV in complex with anagliptin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WQH
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: SKK, NAG
Pockets: 13 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	728	18% helix, 36% strand	P27487

Ligands and binding sites

SKK · N-[2-({2-[(2S)-2-cyanopyrrolidin-1-yl]-2-oxoethyl}amino)-2-methylpropyl]-2-methylpyrazolo[1,5-a]pyrimidine-6-carboxamide · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B

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

Pockets

13 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	64	0.73	0.98	22	empty
2	724	0.69	0.76	89	SKK
3	631	0.68	0.77	79	SKK
4	414	0.57	0.74	56	empty
5	463	0.56	0.72	54	empty

Interfaces

1 interface between chains.

A–B · 2302 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3WQH · Crystal Structure of human DPP-IV in complex with Anagliptin · the same entry in another collection · chain B against B, 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 3WQH · PDBe 3WQH · UniProt P27487

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