4DYM | pdb_00004dym

Crystal structure of the ACVR1 kinase domain in complex with the imidazo[1,2-b]pyridazine inhibitor K00135

• PDB DOI: https://doi.org/10.2210/pdb4DYM/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-02-29 Released: 2012-03-21 
• Deposition Author(s): Chaikuad, A., Sanvitale, C., Cooper, C., Canning, P., Mahajan, P., Daga, N., Petrie, K., Alfano, I., Gileadi, O., Fedorov, O., Krojer, T., Filippakopoulos, P., Muniz, J.R.C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.279 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ACVR1 kinase domain in complex with the imidazo[1,2-b]pyridazine inhibitor K00135

Chaikuad, A., Sanvitale, C., Cooper, C., Canning, P., Mahajan, P., Daga, N., Petrie, K., Alfano, I., Gileadi, O., Fedorov, O., Krojer, T., Filippakopoulos, P., Muniz, J.R.C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.4 kDa 
• Atom Count: 2,487 
• Modeled Residue Count: 293 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-1	A	301	Homo sapiens	Mutation(s): 1  Gene Names: ACVR1, ACVRLK2 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q04771 (Homo sapiens) Explore Q04771  Go to UniProtKB:  Q04771
PHAROS:  Q04771 GTEx:  ENSG00000115170

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IYZ	D [auth A]	1-(3-{6-[(CYCLOPROPYLMETHYL)AMINO]IMIDAZO[1,2-B]PYRIDAZIN-3-YL}PHENYL)ETHANONE C18 H18 N4 O IVUBNTNWKIPCPS-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.279 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.8	α = 90
b = 81.86	β = 90
c = 140.39	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Chaikuad, A., Sanvitale, C., Cooper, C., Canning, P., Mahajan, P., Daga, N., Petrie, K., Alfano, I., Gileadi, O., Fedorov, O., Krojer, T., Filippakopoulos, P., Muniz, J.R.C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description