4FFW

Crystal Structure of Dipeptidyl Peptidase IV (DPP4, DPP-IV, CD26) in Complex with Fab + sitagliptin

• PDB DOI: https://doi.org/10.2210/pdb4FFW/pdb

• Classification: HYDROLASE/Immune System, INHIBITOR
• Organism(s): Rattus norvegicus, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-06-01 Released: 2012-12-12 
• Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P., Min, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.311 
• R-Value Work: 0.287 
• R-Value Observed: 0.288 

Literature

An Inhibitory Antibody Against DPP IV Improves Glucose Tolerance in vivo - Validation of Large Molecule Approach for DPP IV Inhibition

Tang, J., Majeti, J., Sudom, A., Xiong, Y., Lu, M., Liu, Q., Higbee, J., Zhang, Y., Wang, Y., Wang, W., Cao, P., Xia, Z., Johnstone, S., Yang, X., Yu, T., Sharkov, N., Walker, N., Tu, H., Shen, W., Wang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 261.89 kDa 
• Atom Count: 18,266 
• Modelled Residue Count: 2,282 
• Deposited Residue Count: 2,314 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	730	Rattus norvegicus	Mutation(s): 0  Gene Names: Dpp4, Cd26 EC: 3.4.14.5
UniProt
Find proteins for P14740 (Rattus norvegicus) Explore P14740  Go to UniProtKB:  P14740

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	C, F [auth L]	210	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	D, E [auth H]	217	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
715	G [auth A], H [auth B]	(2R)-4-OXO-4-[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-A MINE C16 H15 F6 N5 O MFFMDFFZMYYVKS-SECBINFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
715	BindingDB:  4FFW	IC50: min: 15, max: 69 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.311 
• R-Value Work: 0.287 
• R-Value Observed: 0.288 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.77	α = 90
b = 200.86	β = 93.64
c = 97.93	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P., Min, X.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2018-06-06
  Changes: Data collection
• Version 1.2: 2021-05-19
  Changes: Derived calculations, Source and taxonomy, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary