- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
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), 0.280 (DCC)
- R-Value Work: 0.220 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.223 (Depositor)
Starting Model:experimental
View more details
This is version 1.1 of the entry. See complete history.
Literature
Download MendeleyCrystal 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.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (IYZ)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
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 | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q04771 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IYZ Query on IYZ Download Ideal Coordinates CCD File | 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 Query on SO4 Download Ideal Coordinates CCD File | B [auth A], C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL Download Ideal Coordinates CCD File
| 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), 0.280 (DCC)
- R-Value Work: 0.220 (Depositor), 0.220 (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 Name | Purpose |
|---|---|
| GDA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
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 (Full details and data files)
- Version 1.0: 2012-03-21
Type: Initial release - Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
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