MolNFT v1 · #95878 · protein

Crystal structure of dpp-IV with compound C3

4J3J · Dipeptidyl peptidase 4: “Crystal structure of dpp-IV with compound C3”. X-ray diffraction, 1 ligand (D3C), 15 pockets (best druggability 0.77). MolNFT v1 #95878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4J3J
Type: protein
Length: 1,452 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: D3C
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	725	17% helix, 36% strand	P27487
B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	727	17% helix, 36% strand	P27487

Ligands and binding sites

D3C · N-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butyl]-6-(trifluoromethyl)-3,4-dihydropyrrolo[1,2-a]pyrazine-2(1H)-carboxamide · ligand · 2 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.77	0.97	24	empty
2	883	0.72	0.76	109	D3C
3	771	0.69	0.76	86	D3C
4	490	0.58	0.73	51	empty
5	231	0.52	0.76	33	empty

Interfaces

1 interface between chains.

A–B · 2280 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4J3J · Crystal Structure of DPP-IV with Compound C3 · 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 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 4J3J · PDBe 4J3J · UniProt P27487

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