4GID

Structure of beta-secretase complexed with inhibitor

PDB DOI: https://doi.org/10.2210/pdb4GID/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-08-08 Released: 2012-10-10
Deposition Author(s): Ghosh, A., Tang, J., Venkateswara, R.K., Yadav, N., Anderson, D., Gavande, N., Huang, X., Terzyan, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.252
R-Value Work: 0.216
R-Value Observed: 0.216

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-based design of highly selective beta-secretase inhibitors: synthesis, biological evaluation, and protein-ligand X-ray crystal structure.

Ghosh, A.K., Venkateswara Rao, K., Yadav, N.D., Anderson, D.D., Gavande, N., Huang, X., Terzyan, S., Tang, J.

(2012) J Med Chem 55: 9195-9207

PubMed: 22954357 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm3008823
Primary Citation of Related Structures:
4GID

PubMed Abstract:
The structure-based design, synthesis, and X-ray structure of protein-ligand complexes of exceptionally potent and selective β-secretase inhibitors are described. The inhibitors are designed specifically to interact with S(1)' active site residues to provide selectivity over memapsin 1 and cathepsin D. Inhibitor 5 has exhibited exceedingly potent inhibitory activity (K(i) = 17 pM) and high selectivity over BACE 2 (>7000-fold) and cathepsin D (>250000-fold). A protein-ligand crystal structure revealed important molecular insight into these selectivities. These interactions may serve as an important guide to design selectivity over the physiologically important aspartic acid proteases.

Organizational Affiliation

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States. akghosh@purdue.edu

Macromolecule Content

Total Structure Weight: 176.14 kDa
Atom Count: 13,617
Modelled Residue Count: 1,549
Deposited Residue Count: 1,552
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C, D	388	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0GH Query on 0GH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	N-[(2S)-1-({(2S,3R)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-3-phenylpropan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide C₃₅ H₄₇ N₅ O₆ S UZFAOTIMARRSKT-TYUOOWEOSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
LPD Query on LPD Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	L-PROLINAMIDE C₅ H₁₀ N₂ O VLJNHYLEOZPXFW-BYPYZUCNSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
0GH	PDBBind: 4GID	Ki: 0.02 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.252
R-Value Work: 0.216
R-Value Observed: 0.216
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.427	α = 90
b = 130.353	β = 97.5
c = 88.401	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2013-08-28
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description