Macromolecule Content

Total Structure Weight: 45.61 kDa
Atom Count: 3,273
Modelled Residue Count: 368
Deposited Residue Count: 405
Unique protein chains: 1

3FKT

Crystal Structure of Human Beta Secretase Complexed with Spiropiperdine Iminohydantoin Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3FKT/pdb
Entry: 3FKT supersedes: 3E3W

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

Deposited: 2008-12-17 Released: 2009-01-20
Deposition Author(s): Munshi, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217
R-Value Work: 0.182
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery and X-ray Crystallographic Analysis of a Iminohydantoin Inhibitor of beta-Secretase

Barrow, J.C., Stauffer, S.R., Rittle, K.E., Ngo, P.L., Yang, M.S., Graham, S., McGaughey, G., Holloway, K., Tugusheva, S.K., Lai, M., Espeseth, A.S., Xu, M., Huang, Q., Zuck, P., Levorse, D.A., Hazuda, D., Vacca, J.P.

(2008) J Med Chem 51: 6259-6262

PubMed: 18811140 Search on PubMed
DOI: https://doi.org/10.1021/jm800914n
Primary Citation of Related Structures:
3FKT

PubMed Abstract:

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): 2 Gene Names: BACE, BACE1, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56817
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SII Query on SII Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-(4-{[4-(cyclohexylamino)-1-(3-fluorophenyl)-2-oxo-1,3,8-triazaspiro[4.5]dec-3-en-8-yl]methyl}phenyl)acetamide C₂₈ H₃₄ F N₅ O₂ VXIOVOURIXSOTD-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
SII	PDBBind: 3FKT	IC50: 2800 (nM) from 1 assay(s)
	BindingDB: 3FKT	IC50: 2800 (nM) from 1 assay(s)
	Binding MOAD: 3FKT	IC50: 2800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217
R-Value Work: 0.182
R-Value Observed: 0.183
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.743	α = 90
b = 128.042	β = 90
c = 76.768	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

This entry supersedes: 3E3W

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: 2018-04-04
Changes: Data collection
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.