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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJ6 (Subject of Investigation/LOI)	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
TTP	D [auth A], G [auth B]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EJ6	BindingDB:  6LKM	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 227.83	α = 90
b = 66.92	β = 103.82
c = 110	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Miyahara, S., Chong, K.T., Suzuki, T.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description