3CCC

Crystal Structure of Human DPP4 in complex with a benzimidazole derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure-based design and synthesis of benzimidazole derivatives as dipeptidyl peptidase IV inhibitors.

Wallace, M.B.Feng, J.Zhang, Z.Skene, R.J.Shi, L.Caster, C.L.Kassel, D.B.Xu, R.Gwaltney, S.L.

(2008) Bioorg Med Chem Lett 18: 2362-2367

  • DOI: https://doi.org/10.1016/j.bmcl.2008.02.071
  • Primary Citation of Related Structures:  
    3CCB, 3CCC

  • PubMed Abstract: 

    A novel series of non-covalent, benzimidazole-based inhibitors of DPP-4 has been developed from a small fragment hit using structure-based drug design. A highly versatile synthetic route was created for the development of SAR, which led to the discovery of potent and selective inhibitors with excellent pharmaceutical properties.


  • Organizational Affiliation

    Takeda San Diego, Drug Discovery, 10410 Science Center Drive, San Diego, CA 92121, USA. michael.wallace@takedasd.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B, C, D
740Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P27487-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7AC
Query on 7AC

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B],
U [auth C],
X [auth D]
7-(aminomethyl)-6-(2-chlorophenyl)-1-methyl-1H-benzimidazole-5-carbonitrile
C16 H13 Cl N4
YJLVMTVZVJSNHG-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
N [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7AC BindingDB:  3CCC IC50: 8 (nM) from 1 assay(s)
PDBBind:  3CCC IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.899α = 90
b = 121.958β = 114.94
c = 144.275γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: 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
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary