4PV7 | pdb_00004pv7

Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4PV7/pdb

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


• Deposited: 2014-03-15 Released: 2015-03-18 
• Deposition Author(s): Xiao, P., Guo, R., Huang, S., Cui, H., Ye, S., Zhang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 
  0.264 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Discovery of dipeptidyl peptidase IV (DPP4) inhibitors based on a novel indole scaffold

Xiao, P., Guo, R., Huang, S., Cui, H., Ye, S., Zhang, Z.

(2014) Chin Chem Lett 25: 673-676

• DOI: https://doi.org/10.1016/j.cclet.2014.03.047

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)

Macromolecule Content 

• Total Structure Weight: 175.33 kDa 
• Atom Count: 11,948 
• Modeled Residue Count: 1,454 
• Deposited Residue Count: 1,504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	752	Homo sapiens	Mutation(s): 0  Gene Names: ADCP2, CD26, DPP4 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
PHAROS:  P27487 GTEx:  ENSG00000197635

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CJP	C [auth A], D [auth B]	1-[2-(2,4-dichlorophenyl)-1-(methylsulfonyl)-1H-indol-3-yl]methanamine C16 H14 Cl2 N2 O2 S MTMKFBZYRGNPDF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free:  0.264 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.815	α = 90
b = 79.815	β = 90
c = 286.756	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Xiao, P., Guo, R., Huang, S., Cui, H., Ye, S., Zhang, Z.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary