MolNFT v1 · #73701 · protein

Crystal structure of human DPP4 bound to tak-986

3O9V · Dipeptidyl peptidase 4: “Crystal structure of human DPP4 bound to tak-986”. X-ray diffraction, 2 ligands (10T, NAG), 20 pockets (best druggability 0.75). MolNFT v1 #73701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3O9V
Type: protein
Length: 2,914 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 4
EC: 3.4.14.5
UniProt: P27487
Ligands: 10T, NAG
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	727	17% helix, 35% strand	P27487
B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	733	18% helix, 37% strand	P27487

Ligands and binding sites

10T · 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	75	0.75	0.98	25	empty
2	54	0.72	0.98	16	empty
3	602	0.68	0.77	76	10T
4	599	0.68	0.77	76	10T
5	568	0.67	0.77	72	10T

Interfaces

3 interfaces between chains.

A–B · 2298 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 2283 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 193 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

3O9V · Crystal Structure of Human DPP4 Bound to TAK-986 · the same entry in another collection · chain D against D, 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 3O9V · PDBe 3O9V · UniProt P27487

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