6TTI

PKM2 in complex with Compound 6

• PDB DOI: https://doi.org/10.2210/pdb6TTI/pdb
• EM Map EMD-10577: EMDB EMDataResource

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-27 Released: 2020-01-15 
• Deposition Author(s): Saur, M., Hartshorn, M.J., Dong, J., Reeks, J., Bunkoczi, G., Jhoti, H., Williams, P.A.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Fragment-based drug discovery using cryo-EM.

Saur, M., Hartshorn, M.J., Dong, J., Reeks, J., Bunkoczi, G., Jhoti, H., Williams, P.A.

(2020) Drug Discov Today 25: 485-490

• PubMed: 31877353 
• DOI: https://doi.org/10.1016/j.drudis.2019.12.006
• Primary Citation of Related Structures:  
  6TSH, 6TSK, 6TTE, 6TTF, 6TTH, 6TTI, 6TTQ


• PubMed Abstract: 
  

  Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. Here, we review the use of cryo-EM in fragment-based drug discovery (FBDD) based on in-house method development. We demonstrate not only that cryo-EM can reveal details of the molecular interactions between fragments and a protein, but also that the current reproducibility, quality, and throughput are compatible with FBDD. We exemplify this using the test system β-galactosidase (Bgal) and the oncology target pyruvate kinase 2 (PKM2).

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Organizational Affiliation: 

Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 241.78 kDa 
• Atom Count: 13,172 
• Modelled Residue Count: 1,664 
• Deposited Residue Count: 2,192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM	A, B, C, D	548	Homo sapiens	Mutation(s): 0  Gene Names: PKM, OIP3, PK2, PK3, PKM2 EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618  Go to UniProtKB:  P14618
PHAROS:  P14618 GTEx:  ENSG00000067225

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBP	F [auth A], I [auth B], L [auth C], O [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
NXE (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C], N [auth D]	~{N}-[3-(trifluoromethyl)-1,2-oxazol-5-yl]ethanamide C6 H5 F3 N2 O2 KKHMJANPVRFCAR-UHFFFAOYSA-N
DMS	G [auth A], J [auth B], M [auth C], P [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.04

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Saur, M., Hartshorn, M.J., Dong, J., Reeks, J., Bunkoczi, G., Jhoti, H., Williams, P.A.

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-05-22
  Changes: Data collection, Database references