2BUB

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

• PDB DOI: https://doi.org/10.2210/pdb2BUB/pdb

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


• Deposited: 2005-06-09 Released: 2006-01-23 
• Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Feurer, A., Hill, O., Matassa, V.G., Metz, G., Rummey, C., Thiemann, M., Edwards, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.329 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 171.46 kDa 
• Atom Count: 12,414 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPB	G [auth A], L [auth B]	N-({(2S)-1-[(3R)-3-AMINO-4-(2-FLUOROPHENYL)BUTANOYL]PYRROLIDIN-2-YL}METHYL)BENZAMIDE C22 H26 F N3 O2 ANQHSFFUNMTTRS-MOPGFXCFSA-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
FPB	BindingDB:  2BUB	IC50: min: 90, max: 410 (nM) from 2 assay(s)
	PDBBind:  2BUB	IC50: 90 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.329 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.486	α = 90
b = 66.773	β = 90
c = 425.407	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-23 
Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Feurer, A., Hill, O., Matassa, V.G., Metz, G., Rummey, C., Thiemann, M., Edwards, P.J.

Revision History  

• Version 1.0: 2006-01-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-08-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2019-07-10
  Changes: Data collection, Derived calculations
• Version 2.2: 2019-07-24
  Changes: Data collection
• Version 2.3: 2019-09-04
  Changes: Data collection
• Version 2.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary