4OD9

Structure of Cathepsin D with inhibitor N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide

PDB DOI: https://doi.org/10.2210/pdb4OD9/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-01-10 Released: 2014-08-13
Deposition Author(s): Graedler, U., Czodrowski, P., Tsaklakidis, C., Klein, M., Maskos, K., Leuthner, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure-based optimization of non-peptidic Cathepsin D inhibitors.

Gradler, U., Czodrowski, P., Tsaklakidis, C., Klein, M., Werkmann, D., Lindemann, S., Maskos, K., Leuthner, B.

(2014) Bioorg Med Chem Lett 24: 4141-4150

PubMed: 25086681 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2014.07.054
Primary Citation of Related Structures:
4OBZ, 4OC6, 4OD9

PubMed Abstract:
We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency in the biochemical CatD assay. However, the most potent analogues showed only micromolar activities in an ex vivo glycosaminoglycan (GAG) release assay in bovine cartilage together with low cellular permeability and suboptimal microsomal stability. This new scaffold can serve as a starting point for further optimization towards in vivo efficacy.

Organizational Affiliation

Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany. Electronic address: ulrich.graedler@merckgroup.com.

Macromolecule Content

Total Structure Weight: 77.89 kDa
Atom Count: 5,848
Modelled Residue Count: 675
Deposited Residue Count: 692
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin D light chain	A, C	103	Homo sapiens	Mutation(s): 0 Gene Names: CPSD, CTSD EC: 3.4.23.5
UniProt & NIH Common Fund Data Resources
Find proteins for P07339 (Homo sapiens) Explore P07339 Go to UniProtKB: P07339
PHAROS: P07339 GTEx: ENSG00000117984
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07339
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P07339-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin D heavy chain	B, D	243	Homo sapiens	Mutation(s): 0 Gene Names: CPSD, CTSD EC: 3.4.23.5
UniProt & NIH Common Fund Data Resources
Find proteins for P07339 (Homo sapiens) Explore P07339 Go to UniProtKB: P07339
PHAROS: P07339 GTEx: ENSG00000117984
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07339
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P07339-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2RZ Query on 2RZ Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth D]	G [auth A], K [auth D]	N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide C₂₉ H₃₄ N₄ O₆ IZIUZEPBXLRZLW-JOCHJYFZSA-N		Interactions Focus chain G [auth A] Focus chain K [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth D] mmCIF format, chain I [auth B] mmCIF format, chain J [auth D]	I [auth B], J [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
2RZ	BindingDB: 4OD9	IC50: min: 58, max: 330 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.48	α = 90
b = 73.1	β = 90
c = 234.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
BUSTER	refinement
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 1.1: 2014-09-10
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-27
Changes: Data collection, Database references, Structure summary