3MSJ | pdb_00003msj

Structure of bace (beta secretase) in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb3MSJ/pdb

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

Deposited: 2010-04-29 Released: 2010-07-14
Deposition Author(s): Madden, J., Kramer, J., Smith, M.A., Barker, J., Godemann, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.208 (Depositor), 0.266 (DCC)
R-Value Work:
0.177 (Depositor), 0.247 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Fragment-based discovery and optimization of BACE1 inhibitors.

Madden, J., Dod, J.R., Godemann, R., Kraemer, J., Smith, M., Biniszkiewicz, M., Hallett, D.J., Barker, J., Dyekjaer, J.D., Hesterkamp, T.

(2010) Bioorg Med Chem Lett 20: 5329-5333

PubMed: 20656487 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.06.089
Primary Citation Related Structures:
3MSJ, 3MSK, 3MSL, 3S2O

PubMed Abstract:
A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.

Organizational Affiliation

Evotec UK Ltd, Abingdon, UK. james.madden@evotec.com

Macromolecule Content

Total Structure Weight: 139.63 kDa
Atom Count: 9,702
Modeled Residue Count: 1,121
Deposited Residue Count: 1,233
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, B, C	411	Homo sapiens	Mutation(s): 2 Gene Names: BACE1 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
EV3 Query on EV3 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain U [auth C] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth C] mmCIF format, chain D [auth A]	D [auth A], L [auth B], U [auth C]	3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol C₁₀ H₁₂ Cl N₃ O NSMVCZCLMLZSOB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain D [auth A] Focus chain L [auth B] Focus chain U [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.208 (Depositor), 0.266 (DCC)
R-Value Work: 0.177 (Depositor), 0.247 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.196	α = 90
b = 98.829	β = 103.36
c = 63.132	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary