3LHG

Bace1 in complex with the aminohydantoin Compound 4g

• PDB DOI: https://doi.org/10.2210/pdb3LHG/pdb

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


• Deposited: 2010-01-22 Released: 2010-04-21 
• Deposition Author(s): Olland, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Pyridinyl aminohydantoins as small molecule BACE1 inhibitors.

Zhou, P., Li, Y., Fan, Y., Wang, Z., Chopra, R., Olland, A., Hu, Y., Magolda, R.L., Pangalos, M., Reinhart, P.H., Turner, M.J., Bard, J., Malamas, M.S., Robichaud, A.J.

(2010) Bioorg Med Chem Lett 20: 2326-2329

• PubMed: 20202842 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.136
• Primary Citation of Related Structures:  
  3LHG


• PubMed Abstract: 
  

  A novel class of pyridinyl aminohydantoins was designed and prepared as highly potent BACE1 inhibitors. Compound (S)-4g showed excellent potency with IC(50) of 20 nM for BACE1. X-ray crystallography indicated that the interaction between pyridine nitrogen and the tryptophan Trp76 was a key feature in the S2' region of the enzyme that contributed to increased potency.

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Organizational Affiliation: 

Department of Chemical Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543-8000, United States. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 46.82 kDa 
• Atom Count: 3,078 
• Modelled Residue Count: 369 
• Deposited Residue Count: 415 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	415	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z81	B [auth A]	(5S)-2-amino-5-(2',5'-difluorobiphenyl-3-yl)-3-methyl-5-pyridin-4-yl-3,5-dihydro-4H-imidazol-4-one C21 H16 F2 N4 O RKYFABJLGJZOBA-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z81	BindingDB:  3LHG	IC50: min: 20, max: 50 (nM) from 2 assay(s)
	PDBBind:  3LHG	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.909	α = 90
b = 104.632	β = 94.89
c = 50.26	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Olland, A.M.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary