2ZJN

Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-chloro-2-isopropoxy-3-methoxy-benzyl)-piperidin-4-yl]-2-(2-methyl-4-sulfamoyl-phenoxy)-acetamide

PDB DOI: https://doi.org/10.2210/pdb2ZJN/pdb

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

Deposited: 2008-03-07 Released: 2009-01-20
Deposition Author(s): Randal, M., Lam, M.B., Fahr, B.T., Romanowski, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.260
R-Value Work: 0.222
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Fragment-based discovery of novel BACE1 inhibitors using Tethering technology

Yang, W., Fucini, R.V., Fahr, B.T., Randal, M., Lind, K.E., Lam, M.B., Lu, W., Lu, Y., Cary, D.R., Romanowski, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 45.78 kDa
Atom Count: 2,966
Modelled Residue Count: 367
Deposited Residue Count: 405
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	Homo sapiens	Mutation(s): 0 Gene Names: BACE1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F1N Query on F1N Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-{1-[5-chloro-3-methoxy-2-(1-methylethoxy)benzyl]piperidin-4-yl}-2-(2-methyl-4-sulfamoylphenoxy)acetamide C₂₅ H₃₄ Cl N₃ O₆ S IWMCULWPLNDDNK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.260
R-Value Work: 0.222
R-Value Observed: 0.224
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.989	α = 90
b = 103.989	β = 90
c = 167.081	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-01-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

2ZJN

Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-chloro-2-isopropoxy-3-methoxy-benzyl)-piperidin-4-yl]-2-(2-methyl-4-sulfamoyl-phenoxy)-acetamide

Fragment-based discovery of novel BACE1 inhibitors using Tethering technology

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)