3H9R

Crystal structure of the kinase domain of type I activin receptor (ACVR1) in complex with FKBP12 and dorsomorphin

Structural Biology Knowledgebase: 3H9R SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3H9R

Classification: ISOMERASE / PROTEIN KINASE

Total Structure Weight: 50916.40

Macromolecule Entities
Molecule Chains Length Organism Details
Activin receptor type-1 A 330 Homo sapiens EC#: 2.7.11.30 IUBMB
Fragment: ACVR1 kinase domain (residue 172-499)
Gene Name(s): ACVR1 Gene View ACVRLK2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Peptidyl-prolyl cis-trans isomerase FKBP1A B 109 Homo sapiens EC#: 5.2.1.8 IUBMB
Fragment: FKBP12
Gene Name(s): FKBP1A Gene View FKBP1 FKBP12
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TAK
Query on TAK

A 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin- 4-ylpyrazolo[1,5-a]pyrimidine
Dorsomorphin (Synonym)
C24 H25 N5 O
XHBVYDAKJHETMP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

A TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TAK IC50: 9.76 - 148.1 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.187
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.35 α = 90.00
b = 62.35 β = 90.00
c = 171.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-30
  • Released Date: 2009-06-02
  • Deposition author(s): Chaikuad, A., Alfano, I., Shrestha, B., Muniz, J.R.C., Petrie, K., Fedorov, O., Phillips, C., Bishop, S., Mahajan, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A., Structural Genomics Consortium (SGC)

Revision History

  • 2012-11-28
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4