Crystal structure of human dpp-iv in complex withsa-(+)- methyl2-(3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl- 7-oxo-5h-pyrrolo[3,4-b]pyridin-6(7h)-yl)acetate

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.0 of the entry. See complete history


Discovery of 7-oxo-pyrrolopyridines as potent and selective inhibitors of dpp4

Wang, W.Devasthale, P.Wang, A.Egan, D.Morgan, N.Cap, M.Fura, A.Klei, H.E.Kish, K.Sun, L.Levesque, P.Zahler, R.Kirby, M.Hamann, L.G.

To be published.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4A, B753Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
PHAROS:  P27487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Protein Feature View
  • Reference Sequence


Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on LGE

Download Ideal Coordinates CCD File 
J [auth A],
P [auth B]
methyl [3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-7-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]acetate
C18 H17 Cl2 N3 O3
 Ligand Interaction
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
C8 H15 N O6
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LGE BindingDB:  3Q0T Ki: min: 2.7, max: 76 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.686α = 90
b = 67.569β = 90
c = 420.978γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2012-02-29 
  • Deposition Author(s): Klei, H.E.

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Non-polymer description
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary