6TU9

The ROR1 Pseudokinase Domain Bound To Ponatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Insights into Pseudokinase Domains of Receptor Tyrosine Kinases.

Sheetz, J.B.Mathea, S.Karvonen, H.Malhotra, K.Chatterjee, D.Niininen, W.Perttila, R.Preuss, F.Suresh, K.Stayrook, S.E.Tsutsui, Y.Radhakrishnan, R.Ungureanu, D.Knapp, S.Lemmon, M.A.

(2020) Mol Cell 79: 390-405.e7

  • DOI: 10.1016/j.molcel.2020.06.018
  • Primary Citation of Related Structures:  
    6TUA, 6TU9

  • PubMed Abstract: 
  • Despite their apparent lack of catalytic activity, pseudokinases are essential signaling molecules. Here, we describe the structural and dynamic properties of pseudokinase domains from the Wnt-binding receptor tyrosine kinases (PTK7, ROR1, ROR2, and ...

    Despite their apparent lack of catalytic activity, pseudokinases are essential signaling molecules. Here, we describe the structural and dynamic properties of pseudokinase domains from the Wnt-binding receptor tyrosine kinases (PTK7, ROR1, ROR2, and RYK), which play important roles in development. We determined structures of all pseudokinase domains in this family and found that they share a conserved inactive conformation in their activation loop that resembles the autoinhibited insulin receptor kinase (IRK). They also have inaccessible ATP-binding pockets, occluded by aromatic residues that mimic a cofactor-bound state. Structural comparisons revealed significant domain plasticity and alternative interactions that substitute for absent conserved motifs. The pseudokinases also showed dynamic properties that were strikingly similar to those of IRK. Despite the inaccessible ATP site, screening identified ATP-competitive type-II inhibitors for ROR1. Our results set the stage for an emerging therapeutic modality of "conformational disruptors" to inhibit or modulate non-catalytic functions of pseudokinases deregulated in disease.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA. Electronic address: mark.lemmon@yale.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inactive tyrosine-protein kinase transmembrane receptor ROR1A, B306Homo sapiensMutation(s): 0 
Gene Names: ROR1NTRKR1
Find proteins for Q01973 (Homo sapiens)
Explore Q01973 
Go to UniProtKB:  Q01973
NIH Common Fund Data Resources
PHAROS  Q01973
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LI
Query on 0LI

Download CCD File 
A, B
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide
C29 H27 F3 N6 O
PHXJVRSECIGDHY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.29α = 90
b = 85.969β = 91.045
c = 72.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2020-08-19
    Changes: Database references