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DPP4 complexed with compound 12A

Analyse DPP4 complexed with compound 12A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N8E
Type: protein
Length: 1,461 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: 2KV, NAG, MAN, SO4
Pockets: 18 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	727	18% helix, 37% strand	P27487
B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	734	18% helix, 37% strand	P27487

Ligands and binding sites

2KV · 1-[cis-4-(aminomethyl)-4-(3-chlorophenyl)cyclohexyl]piperidin-2-one · 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 · 3 copies
SO4 · Sulfate ion · ion · 6 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.77	0.98	22	empty
2	738	0.70	0.77	88	2KV
3	713	0.70	0.77	78	2KV
4	377	0.57	0.75	51	empty
5	106	0.49	0.81	16	empty

Interfaces

1 interface between chains.

A–B · 2351 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 glycan, 10 disulfide (N-glycosylation, disulfide).

Compared structures

4N8E · DPP4 complexed with compound 12a · 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 4N8E · PDBe 4N8E · UniProt P27487

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