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Crystal structure of human dpp-IV in complex with sa-(+)-3- (aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)- 2-methyl- 5H-PYRROLO[3,4-B]PYRIDIN-7(6H)-one

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

PDB: 3SWW
Type: protein
Length: 1,454 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: KXB, NAG
Pockets: 19 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).

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

Ligands and binding sites

KXB · 3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyethyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B

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

Pockets

19 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	73	0.74	0.97	23	empty
2	541	0.66	0.77	67	KXB
3	481	0.65	0.77	62	KXB
4	196	0.51	0.77	30	empty
5	204	0.50	0.76	27	empty

Interfaces

1 interface between chains.

A–B · 2293 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 glycan, 10 disulfide (N-glycosylation, disulfide).

Compared structures

3SWW · Crystal structure of human dpp-iv in complex with… · 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 3SWW · PDBe 3SWW · UniProt P27487

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