MolNFT v1 · #147821 · protein

DPP9 - 1G244

6EOR · Dipeptidyl peptidase 9: “DPP9 - 1G244”. X-ray diffraction, 1 ligand (9XH), 20 pockets (best druggability 0.84). MolNFT v1 #147821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6EOR
Type: protein
Length: 3,233 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 9
EC: 3.4.14.5
UniProt: Q86TI2
Ligands: 9XH
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	808	18% helix, 33% strand	Q86TI2
B	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	805	18% helix, 34% strand	Q86TI2
C	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	808	18% helix, 34% strand	Q86TI2
D	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	812	19% helix, 35% strand	Q86TI2

Ligands and binding sites

9XH · (2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl) methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl) butane-1,4-dione · ligand · 4 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.84	0.98	32	empty
2	194	0.84	0.98	32	empty
3	971	0.81	0.83	78	empty
4	564	0.80	0.86	58	empty
5	1120	0.79	0.81	122	9XH

Interfaces

4 interfaces between chains.

C–D · 2214 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2202 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 644 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 632 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6EOR · DPP9 - 1G244 · the same entry in another collection · chain D against D, TM-score 1.00
Q86TI2 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 9 (Q86TI2) · a predicted model of the same protein · chain C 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 Q86TI2
Elsewhere: RCSB PDB 6EOR · PDBe 6EOR · UniProt Q86TI2

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