4B0Q | pdb_00004b0q

Lead Generation of BACE1 Inhibitors by Coupling Non-amidine New Warheads to a Known Binding Scaffold

PDB DOI: https://doi.org/10.2210/pdb4B0Q/pdb

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

Deposited: 2012-07-04 Released: 2013-07-24
Deposition Author(s): Pendrill, R., Kolmodin, K., Johansson, P., Plobeck, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.225 (Depositor), 0.212 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Lead Generation of Bace1 Inhibitors by Coupling Non-Amidine New Warheads to a Known Binding Scaffold

Pendrill, R., Kolmodin, K., Johansson, P., Plobeck, N.

To be published.

Macromolecule Content

Total Structure Weight: 43.32 kDa
Atom Count: 3,267
Modeled Residue Count: 369
Deposited Residue Count: 384
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	384	Homo sapiens	Mutation(s): 0 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GMF Query on GMF Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[[3-(3-methoxyphenyl)phenyl]-(4-pyridyl)methyl]guanidine C₂₀ H₂₀ N₄ O LSPQISZRKHVJOD-LJQANCHMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.225 (Depositor), 0.212 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.571	α = 90
b = 76.277	β = 90
c = 103.939	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, Structure summary

4B0Q | pdb_00004b0q

Lead Generation of BACE1 Inhibitors by Coupling Non-amidine New Warheads to a Known Binding Scaffold

Literature

Lead Generation of Bace1 Inhibitors by Coupling Non-Amidine New Warheads to a Known Binding Scaffold

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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