5OY6

Crystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor OD36.

PDB DOI: https://doi.org/10.2210/pdb5OY6/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2017-09-07 Released: 2017-09-27
Deposition Author(s): Williams, E.P., Pinkas, D.M., Krojer, T., Kupinska, K., Mahajan, P., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Establishment and characterization of endothelial colony forming cells as a surrogate model for Fibrodysplasia Ossificans Progressiva

Sanchez-Duffhues, G., Orlova, V., Benderitter, P., Williams, E.P., Garcia de Vinuesa, A., Caradec, J., van Wijhe, M., de Boer, H., Goumans, M.J., Eeckhoff, M., Morales Piga, A., Bachiller, J., Koolwijk, P., Bullock, A., Hoflack, J., ten Dijke, P.

To be published.

Macromolecule Content

Total Structure Weight: 139.6 kDa
Atom Count: 9,043
Modelled Residue Count: 1,166
Deposited Residue Count: 1,204
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-1	A, B, C, D	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B4E Query on B4E Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D]	E [auth A], H [auth B], I [auth C], J [auth D]	cyclical inhibitor OD36 C₁₆ H₁₅ Cl N₄ O₂ KTSDBMVHAKWDRK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.213
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.26	α = 90
b = 103.53	β = 116.52
c = 84.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2017-12-13
Changes: Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description

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Help and Resources

5OY6

Crystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor OD36.

Establishment and characterization of endothelial colony forming cells as a surrogate model for Fibrodysplasia Ossificans Progressiva

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)