3N0T

Human dipeptidil peptidase DPP7 complexed with inhibitor GSK237826A

• PDB DOI: https://doi.org/10.2210/pdb3N0T/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-05-14 Released: 2010-07-21 
• Deposition Author(s): Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Crombet, L., Cossar, D., Pagannon, S., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hassell, A., Shewchuk, L., Haffner, C., Bochkarev, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.260 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

Human dipeptidyl peptidase DPP7

Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Crombet, L., Cossar, D., Pagannon, S., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Hassell, A., Shewchuk, L., Haffner, C., Bochkarev, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 208.91 kDa 
• Atom Count: 14,133 
• Modelled Residue Count: 1,804 
• Deposited Residue Count: 1,876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 2	A, B, C, D	469	Homo sapiens	Mutation(s): 0  Gene Names: DPP2, DPP7, QPP EC: 3.4.14.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHL4 (Homo sapiens) Explore Q9UHL4  Go to UniProtKB:  Q9UHL4
PHAROS:  Q9UHL4 GTEx:  ENSG00000176978

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OPY	E [auth A], F [auth B], G [auth C], H [auth D]	(3S)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine C9 H19 N3 O RKBKYSFKXFKBBM-QMMMGPOBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OPY	BindingDB:  3N0T	IC50: min: 130, max: 1.91e+5 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.260 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.546	α = 90
b = 130.5	β = 102.28
c = 125.075	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
MOLREP	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Crombet, L., Cossar, D., Pagannon, S., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hassell, A., Shewchuk, L., Haffner, C., Bochkarev, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary