3H0C

Crystal Structure of Human Dipeptidyl Peptidase IV (CD26) in Complex with a Reversed Amide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3H0C/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-04-09 Released: 2009-06-09 
• Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Deppe, H., Hill, O., Lopez-Canet, M., Rummey, C., Thiemann, M., Matassa, V.G., Edwards, P.J., Feurer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.271 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Discovery of b-homophenylalanine based pyrrolidin-2-ylmethyl amides and sulfonamides as highly potent and selective inhibitors of dipeptidyl peptidase IV

Nordhoff, S., Cerezo-Galvez, S., Deppe, H., Hill, O., Lopez-Canet, M., Rummey, C., Thiemann, M., Matassa, V.G., Edwards, P.J., Feurer, 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)

Macromolecule Content

• Total Structure Weight: 171.65 kDa 
• Atom Count: 12,460 
• Modelled Residue Count: 1,456 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	728	Homo sapiens	Mutation(s): 0  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
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P27487-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PS4	G [auth A], L [auth B]	N-({(2S)-1-[(3R)-3-amino-4-(3-chlorophenyl)butanoyl]pyrrolidin-2-yl}methyl)-3-(methylsulfonyl)benzamide C23 H28 Cl N3 O4 S QRGBOABBMKYMLG-UXHICEINSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PS4	BindingDB:  3H0C	IC50: 0.38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.271 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.694	α = 90
b = 67.072	β = 90
c = 425.135	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Deppe, H., Hill, O., Lopez-Canet, M., Rummey, C., Thiemann, M., Matassa, V.G., Edwards, P.J., Feurer, A.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary