MolNFT v1 · #37749 · protein

Rat dpp-IV with alkynyl cyanopyrrolidine #1

2GBF · Dipeptidyl peptidase 4: “Rat dpp-IV with alkynyl cyanopyrrolidine #1”. X-ray diffraction, 1 ligand (AIA), 12 pockets (best druggability 0.78). MolNFT v1 #37749 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GBF
Type: protein
Length: 1,460 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: P14740
Ligands: AIA
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	730	17% helix, 36% strand	P14740

Ligands and binding sites

AIA · (1S)-2-[(2S,5R)-2-(aminomethyl)-5-ethynylpyrrolidin-1-yl]-1-cyclopentyl-2-oxoethanamine · ligand · chains A

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

Pockets

12 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	163	0.78	0.94	33	empty
2	833	0.72	0.77	105	AIA
3	689	0.68	0.76	76	empty
4	398	0.56	0.74	53	empty
5	195	0.51	0.77	32	empty

Interfaces

1 interface between chains.

A–B · 2180 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

2GBF · rat dpp-IV with alkynyl cyanopyrrolidine #1 · the same entry in another collection · chain A against A, TM-score 1.00
P14740 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P14740) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P14740
Elsewhere: RCSB PDB 2GBF · PDBe 2GBF · UniProt P14740

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