4I0I | pdb_00004i0i

SPR and structural analysis yield insight towards mechanism of inhibition of BACE inhibitors

PDB DOI: https://doi.org/10.2210/pdb4I0I/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-16 Released: 2013-11-20
Deposition Author(s): Yao, N., Brecht, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.279 (Depositor), 0.266 (DCC)
R-Value Work:
0.231 (Depositor), 0.220 (DCC)
R-Value Observed:
0.233 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

SPR and structural analysis yield insight towards mechanism of inhibition of BACE inhibitors

Mondal, K., Regnstrom, K., Morishige, W., Barbour, R., Beroza, P., Yao, N., Bova, M.P.

To be published.

Macromolecule Content

Total Structure Weight: 137.69 kDa
Atom Count: 9,293
Modeled Residue Count: 1,124
Deposited Residue Count: 1,218
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	406	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
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
957 Query on 957 Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	N-[(1S,2R)-1-(3,5-difluorobenzyl)-3-({1-[4-(2,2-dimethylpropyl)thiophen-2-yl]cyclopropyl}amino)-2-hydroxypropyl]acetamide C₂₄ H₃₂ F₂ N₂ O₂ S YEGCCSKZPHGALE-LEWJYISDSA-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: 2.20 Å
R-Value Free: 0.279 (Depositor), 0.266 (DCC)
R-Value Work: 0.231 (Depositor), 0.220 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.155	α = 90
b = 104.592	β = 104.5
c = 100.155	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-11-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.