6IZP | pdb_00006izp

Solution structure of the complex of naphthyridine carbamate dimer and an RNA with UGGAA-UGGAA pentad

PDB DOI: https://doi.org/10.2210/pdb6IZP/pdb
NAKB: 6IZP

Classification: RNA
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2018-12-20 Released: 2019-12-25
Deposition Author(s): Nagano, K., Shibata, T., Nakatani, K., Kawai, G.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 6IZP

This is version 1.3 of the entry. See complete history.

Literature

Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model

Shibata, T., Nagano, K., Ueyama, M., Ninomiya, K., Hirose, T., Nagai, Y., Ishikawa, K., Kawai, G., Nakatani, K.

(2021) Nat Commun 12

DOI: https://doi.org/10.1038/s41467-020-20487-4

Macromolecule Content

Total Structure Weight: 10.33 kDa
Atom Count: 691
Modeled Residue Count: 29
Deposited Residue Count: 29
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (29-MER)	A	29	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B2R (Subject of Investigation/LOI) Query on B2R Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	3-[3-[(7-methyl-1,8-naphthyridin-2-yl)carbamoyloxy]propylamino]propyl ~{N}-(7-methyl-1,8-naphthyridin-2-yl)carbamate C₂₆ H₂₉ N₇ O₄ RLXLNYXAIXVZCE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2021-01-20
Changes: Database references
Version 1.2: 2023-06-14
Changes: Database references, Other
Version 1.3: 2024-05-15
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.