7A3K

Crystal structure of DPP8 in complex with a b-lactam based inhibitor, A296.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QX8Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Discovery and Development of 4-Oxo-beta-Lactams as Novel Inhibitors of Dipeptidyl Peptidases 8 and 9

Fehr, L.Carvalho, L.A.R.Ross, B.H.Lum, K.Vieira, A.C.Kiefersauer, R.Geiss-Friedlander, R.Kaiser, M.Rodrigues, T.Lucas, S.D.Cravatt, B.F.Huber, R.Moreira, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 8A [auth C],
B [auth A],
C [auth B]
898Homo sapiensMutation(s): 0 
Gene Names: DPP8DPRP1MSTP097MSTP135MSTP141
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q6V1X1 (Homo sapiens)
Explore Q6V1X1 
Go to UniProtKB:  Q6V1X1
PHAROS:  Q6V1X1
GTEx:  ENSG00000074603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6V1X1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QX8 (Subject of Investigation/LOI)
Query on QX8

Download Ideal Coordinates CCD File 
J [auth C],
O [auth A],
T [auth B]
1-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]azetidin-2-one
C21 H24 Br N3 O
UKZMZNGKMQQUCK-UHFFFAOYSA-N
TMO
Query on TMO

Download Ideal Coordinates CCD File 
D [auth C],
K [auth A],
P [auth B]
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth C]
F [auth C]
G [auth C]
H [auth C]
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth C],
N [auth A],
S [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.264α = 90
b = 250.38β = 90
c = 261.202γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QX8Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description