MolNFT v1 · #89541 · protein

Crystal structure of dpp-IV with compound C1

4DSA · Dipeptidyl peptidase 4: “Crystal structure of dpp-IV with compound C1”. X-ray diffraction, 1 ligand (D1C), 14 pockets (best druggability 0.78). MolNFT v1 #89541 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DSA
Type: protein
Length: 1,448 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: D1C
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	724	19% helix, 37% strand	P27487

Ligands and binding sites

D1C · 4-[({[(2R)-2-amino-3-(2,4,5-trifluorophenyl)propyl]sulfamoyl}amino)methyl]benzenesulfonamide · ligand · chains A

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.78	0.98	22	empty
2	731	0.69	0.76	82	empty
3	731	0.69	0.76	93	D1C
4	472	0.57	0.73	58	empty
5	343	0.53	0.74	45	empty

Interfaces

1 interface between chains.

A–B · 2279 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4DSA · Crystal Structure of DPP-IV with Compound C1 · 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 4DSA · PDBe 4DSA · UniProt P27487

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