4FCO | pdb_00004fco

Crystal structure of bace1 with its inhibitor

PDB DOI: https://doi.org/10.2210/pdb4FCO/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-05-25 Released: 2013-05-29
Deposition Author(s): Chen, T.T., Chen, W.Y., Li, L., Xu, Y.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.183 (Depositor), 0.182 (DCC)
R-Value Work:
0.163 (Depositor), 0.161 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations

Xu, Y.C., Chen, W.Y., Chen, T.T., Li, L.

To be published.

Macromolecule Content

Total Structure Weight: 49.37 kDa
Atom Count: 3,437
Modeled Residue Count: 374
Deposited Residue Count: 433
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	433	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 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0U4 Query on 0U4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	N-[(2S,3R)-4-{[2-(1-benzylpiperidin-4-yl)ethyl]amino}-3-hydroxy-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide C₄₂ H₅₃ N₅ O₅ S IMNAYTZSJCRZIO-RLRCJDGOSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
URE Query on URE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
0U4	BindingDB: 4FCO	IC50: min: 99, max: 567 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.183 (Depositor), 0.182 (DCC)
R-Value Work: 0.163 (Depositor), 0.161 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.44	α = 90
b = 128.42	β = 90
c = 76.27	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

4FCO | pdb_00004fco

Crystal structure of bace1 with its inhibitor

Literature

Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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