2ZJK | pdb_00002zjk

Crystal structure of the human BACE1 catalytic domain in complex with 4-(4-fluoro-benzyl)-piperazine-2-carboxylic acid(3-mercapto-propyl)-amide

PDB DOI: https://doi.org/10.2210/pdb2ZJK/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.293 (Depositor), 0.278 (DCC)
R-Value Work:
0.247 (Depositor), 0.237 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2ZJK

Ligand Structure Quality Assessment

This is version 1.4 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: 136.66 kDa
Atom Count: 8,697
Modeled Residue Count: 1,111
Deposited Residue Count: 1,215
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	405	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F1K Query on F1K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	(2S)-4-(4-fluorobenzyl)-N-(3-sulfanylpropyl)piperazine-2-carboxamide C₁₅ H₂₂ F N₃ O S OYTFYWWLBPDTNS-AWEZNQCLSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.293 (Depositor), 0.278 (DCC)
R-Value Work: 0.247 (Depositor), 0.237 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233.149	α = 90
b = 108.546	β = 103.34
c = 64.091	γ = 90

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Romanowski, M.J.

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: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.