6FER | pdb_00006fer

Crystal Structure of human DDR2 kinase in complex with 2-[4,5-difluoro-2-oxo-1'-(1H-pyrazolo[3,4-b]pyridine-5-carbonyl)spiro[indole-3,4'-piperidine]-1-yl]-N-(2,2,2-trifluoroethyl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 
    0.287 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome.

Richter, H.Satz, A.L.Bedoucha, M.Buettelmann, B.Petersen, A.C.Harmeier, A.Hermosilla, R.Hochstrasser, R.Burger, D.Gsell, B.Gasser, R.Huber, S.Hug, M.N.Kocer, B.Kuhn, B.Ritter, M.Rudolph, M.G.Weibel, F.Molina-David, J.Kim, J.J.Santos, J.V.Stihle, M.Georges, G.J.Bonfil, R.D.Fridman, R.Uhles, S.Moll, S.Faul, C.Fornoni, A.Prunotto, M.

(2019) ACS Chem Biol 14: 37-49

  • DOI: https://doi.org/10.1021/acschembio.8b00866
  • Primary Citation Related Structures: 
    6FER, 6FEW, 6FEX, 6FIL, 6FIN, 6FIO, 6FIQ

  • PubMed Abstract: 

    The importance of Discoidin Domain Receptor 1 (DDR1) in renal fibrosis has been shown via gene knockout and use of antisense oligonucleotides; however, these techniques act via a reduction of DDR1 protein, while we prove the therapeutic potential of inhibiting DDR1 phosphorylation with a small molecule. To date, efforts to generate a selective small-molecule to specifically modulate the activity of DDR1 in an in vivo model have been unsuccessful. We performed parallel DNA encoded library screens against DDR1 and DDR2, and discovered a chemical series that is highly selective for DDR1 over DDR2. Structure-guided optimization efforts yielded the potent DDR1 inhibitor 2.45, which possesses excellent kinome selectivity (including 64-fold selectivity over DDR2 in a biochemical assay), a clean in vitro safety profile, and favorable pharmacokinetic and physicochemical properties. As desired, compound 2.45 modulates DDR1 phosphorylation in vitro as well as prevents collagen-induced activation of renal epithelial cells expressing DDR1. Compound 2.45 preserves renal function and reduces tissue damage in Col4a3 -/- mice (the preclinical mouse model of Alport syndrome) when employing a therapeutic dosing regime, indicating the real therapeutic value of selectively inhibiting DDR1 phosphorylation in vivo. Our results may have wider significance as Col4a3 -/- mice also represent a model for chronic kidney disease, a disease which affects 10% of the global population.


  • Organizational Affiliation
    • Roche Pharma Research and Early Development, Roche Innovation Center , Basel 4070 , Switzerland.

Macromolecule Content 

  • Total Structure Weight: 435.19 kDa 
  • Atom Count: 27,069 
  • Modeled Residue Count: 3,275 
  • Deposited Residue Count: 3,708 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Discoidin domain-containing receptor 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
309Homo sapiensMutation(s): 0 
Gene Names: DDR2NTRKR3TKTTYRO10
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16832 (Homo sapiens)
Explore Q16832 
Go to UniProtKB:  Q16832
PHAROS:  Q16832
GTEx:  ENSG00000162733 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16832
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D6Q

Query on D6Q



Download:Ideal Coordinates CCD File
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
2-[4,5-bis(fluoranyl)-2-oxidanylidene-1'-(1~{H}-pyrazolo[3,4-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide
C23 H19 F5 N6 O3
IJPAFYMYOCLEBL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free:  0.287 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.91α = 90
b = 155.79β = 90
c = 355.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description