6ACR | pdb_00006acr

Crystal structure of human ALK2 kinase domain with R206H mutation in complex with RK-59638

PDB DOI: https://doi.org/10.2210/pdb6ACR/pdb

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

Deposited: 2018-07-27 Released: 2019-03-20
Deposition Author(s): Sakai, N., Mishima-Tsumagari, C., Matsumoto, T., Shirouzu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.213 (Depositor), 0.214 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Bis-Heteroaryl Pyrazoles: Identification of Orally Bioavailable Inhibitors of Activin Receptor-Like Kinase-2 (R206H).

Sekimata, K., Sato, T., Sakai, N., Watanabe, H., Mishima-Tsumagari, C., Taguri, T., Matsumoto, T., Fujii, Y., Handa, N., Honma, T., Tanaka, A., Shirouzu, M., Yokoyama, S., Miyazono, K., Hashizume, Y., Koyama, H.

(2019) Chem Pharm Bull (Tokyo) 67: 224-235

PubMed: 30828000 Search on PubMed
DOI: https://doi.org/10.1248/cpb.c18-00598
Primary Citation Related Structures:
6ACR

PubMed Abstract:
Mutant activin receptor-like kinase-2 (ALK2) was reported to be closely associated with the pathogenesis of fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG), and therefore presents an attractive target for therapeutic intervention. Through in silico virtual screenings and structure-activity relationship studies assisted by X-ray crystallographic analyses, a novel series of bis-heteroaryl pyrazole was identified as potent inhibitors of ALK2 (R206H). Derived from in silico hit compound RK-59638 (6a), compound 18p was identified as a potent inhibitor of ALK2 (R206H) with good aqueous solubility, liver microsomal stability, and oral bioavailability.

Organizational Affiliation

Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science.

Macromolecule Content

Total Structure Weight: 70.33 kDa
Atom Count: 4,903
Modeled Residue Count: 587
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-1	A, B	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04771
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9TO Query on 9TO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	N-(4-methoxyphenyl)-4-[3-(pyridin-3-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine C₁₉ H₁₆ N₆ O ANTWQGSNXAZMBT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]