6LKM | pdb_00006lkm

Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 5-chloro-N-((1S,2R)-2-(6-fluoro-2,3-dimethylphenyl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)-4-methyl-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-sulfonamide

PDB DOI: https://doi.org/10.2210/pdb6LKM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-19 Released: 2020-12-23
Deposition Author(s): Miyahara, S., Chong, K.T., Suzuki, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.277 (Depositor), 0.277 (DCC)
R-Value Work:
0.210 (Depositor), 0.214 (DCC)
R-Value Observed:
0.213 (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

TAS1553, a novel small molecule ribonucleotide reductase (RNR) subunit interaction inhibitor, displays remarkable anti-tumor activity

Miyahara, S., Hara, S., Chong, K.T., Suzuki, T., Ogino, Y., Hoshino, T., Tsukioka, S., Yano, W., Suzuki, M., Otsu, Y., Yonekura, T., Ito, S., Terasaka, M., Suzuki, T., Hashimoto, A.

To be published.

Macromolecule Content

Total Structure Weight: 154.41 kDa
Atom Count: 10,700
Modeled Residue Count: 1,333
Deposited Residue Count: 1,338
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase large subunit	A, B	669	Homo sapiens	Mutation(s): 0 Gene Names: RRM1, RR1 EC: 1.17.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23921 (Homo sapiens) Explore P23921 Go to UniProtKB: P23921
PHAROS: P23921 GTEx: ENSG00000167325
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23921
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EJ6 (Subject of Investigation/LOI) Query on EJ6 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	5-chloro-N-((1S,2R)-2-(6-fluoro-2,3-dimethylphenyl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)-4-methyl-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-sulfonamide C₂₂ H₂₄ Cl F N₄ O₅ S OODUGOCGSLORQM-ACJLOTCBSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
TTP Query on TTP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	THYMIDINE-5'-TRIPHOSPHATE C₁₀ H₁₇ N₂ O₁₄ P₃ NHVNXKFIZYSCEB-XLPZGREQSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]