3VJL

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #2

• PDB DOI: https://doi.org/10.2210/pdb3VJL/pdb

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


• Deposited: 2011-10-24 Released: 2012-10-24 
• Deposition Author(s): Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

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: 176.17 kDa 
• Atom Count: 13,126 
• Modelled Residue Count: 1,458 
• Deposited Residue Count: 1,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	740	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W94	H [auth A], L [auth B]	[(2S,4S)-4-{4-[1-phenyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]piperidin-1-yl}pyrrolidin-2-yl](1,3-thiazolidin-3-yl)methanone C23 H28 F3 N5 O S CYNIHEXFNGMKLP-OALUTQOASA-N
NAG	I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
W94	PDBBind:  3VJL	IC50: 5.6 (nM) from 1 assay(s)
	BindingDB:  3VJL	IC50: min: 2.5, max: 5.6 (nM) from 2 assay(s)
	Binding MOAD:  3VJL	IC50: 5.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.81	α = 90
b = 125.83	β = 90
c = 137.129	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary