2Q6B

Design and synthesis of novel, conformationally restricted HMG-COA reductase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2Q6B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-04 Released: 2007-07-17 
• Deposition Author(s): Pavlovsky, A., Pfefferkorn, J.A., Harris, M.S., Finzel, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Design and synthesis of novel, conformationally restricted HMG-CoA reductase inhibitors.

Pfefferkorn, J.A., Choi, C., Song, Y., Trivedi, B.K., Larsen, S.D., Askew, V., Dillon, L., Hanselman, J.C., Lin, Z., Lu, G., Robertson, A., Sekerke, C., Auerbach, B., Pavlovsky, A., Harris, M.S., Bainbridge, G., Caspers, N.

(2007) Bioorg Med Chem Lett 17: 4531-4537

• PubMed: 17574411 
• DOI: https://doi.org/10.1016/j.bmcl.2007.05.097
• Primary Citation of Related Structures:  
  2Q6B, 2Q6C


• PubMed Abstract: 
  

  Using structure-based design, a novel series of conformationally restricted, pyrrole-based inhibitors of HMG-CoA reductase were discovered. Leading analogs demonstrated potent inhibition of cholesterol synthesis in both in vitro and in vivo models and may be useful for the treatment of hypercholesterolemia and related lipid disorders.

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Organizational Affiliation: 

Pfizer Global Research & Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. [e-mail]

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: 192.39 kDa 
• Atom Count: 13,820 
• Modelled Residue Count: 1,688 
• Deposited Residue Count: 1,764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxy-3-methylglutaryl-coenzyme A reductase	A, B, C, D	441	Homo sapiens	Mutation(s): 1  Gene Names: HMGCR EC: 1.1.1.34
UniProt & NIH Common Fund Data Resources
Find proteins for P04035 (Homo sapiens) Explore P04035  Go to UniProtKB:  P04035
PHAROS:  P04035 GTEx:  ENSG00000113161

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HR2	F [auth A], G [auth A], J [auth C], L [auth D]	(3R,5R)-7-[3-(4-FLUOROPHENYL)-1-ISOPROPYL-8-OXO-7-PHENYL-1,4,5,6,7,8-HEXAHYDROPYRROLO[2,3-C]AZEPIN-2-YL]-3,5-DIHYDROXYHEPTANOIC ACID C30 H35 F N2 O5 OMBVEVHRIQULKW-DNQXCXABSA-N
SO4	E [auth A], H [auth B], I [auth C], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
HR2	PDBBind:  2Q6B	IC50: 0.3 (nM) from 1 assay(s)
	BindingDB:  2Q6B	-TΔS: min: -2.13e+1, max: 19.22 (kJ/mol) from 3 assay(s)
		ΔG: min: -4.72e+1, max: -4.26e+1 (kJ/mol) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.724	α = 90
b = 133.186	β = 92.63
c = 82.673	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Pavlovsky, A., Pfefferkorn, J.A., Harris, M.S., Finzel, B.C.

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-21
  Changes: Data collection