3KYR | pdb_00003kyr

Bace-1 in complex with a norstatine type inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3KYR/pdb

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


• Deposited: 2009-12-07 Released: 2010-12-29 
• Deposition Author(s): Lindberg, J.D., Borkakoti, N., Derbyshire, D., Nystrom, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Investigation of a-phenylnorstatine and a-benzylnorstatine as transition state isostere motifs in the search for new BACE-1 inhibiotrs

Wangsell, F., Nordeman, P., Savmarker, J., Emanuelsson, R., Jansson, K., Lindberg, J., Rosenqvist, A., Samuelsson, B., Larhed, M.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.96 kDa 
• Atom Count: 8,802 
• Modeled Residue Count: 1,088 
• Deposited Residue Count: 1,215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	405	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
038	D [auth A], E [auth B], F [auth C]	3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-azanyl-3-(1H-1,2,3,4-tetrazol-5-ylcarbonylamino)propanoyl]amino]-3-methyl-butanoyl]amino]-4-methyl-pentanoyl]amino]methyl]-2-hydroxy-4-phenyl-butanoyl]amino]benzoic acid C34 H46 N10 O8 FZZOBXKGDCMGAL-NAJARDBOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
038	BindingDB:  3KYR	IC50: 190 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001038 (038)	D [auth A], E [auth B], F [auth C]	3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-AZANYL-3-(1H-1,2,3,4-TETRAZOL-5-YLCARBONYLAMINO)PROPANOYL]AMINO]-3-METHYL-BUTANOYL]AMINO]-4-METHYL-PENTANOYL]AMINO]METHYL]-2-HYDROXY-4-PHENYL-BUTANOYL]AMINO]BENZOIC ACID	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.762	α = 90
b = 102.774	β = 102.9
c = 101.427	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Lindberg, J.D., Borkakoti, N., Derbyshire, D., Nystrom, S.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary