4N7E

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469

PDB DOI: https://doi.org/10.2210/pdb4N7E/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2013-10-15 Released: 2014-01-22
Deposition Author(s): Andersen, J.L., Strandbygaard, D., Thirup, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.242
R-Value Work: 0.201
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The identification of AF38469: An orally bioavailable inhibitor of the VPS10P family sorting receptor Sortilin.

Schrder, T.J., Christensen, S., Lindberg, S., Langgard, M., David, L., Maltas, P.J., Eskildsen, J., Jacobsen, J., Tagmose, L., Simonsen, K.B., Biilmann Rnn, L.C., de Jong, I.E., Malik, I.J., Karlsson, J.J., Bundgaard, C., Egebjerg, J., Stavenhagen, J.B., Strandbygard, D., Thirup, S., Andersen, J.L., Uppalanchi, S., Pervaram, S., Kasturi, S.P., Eradi, P., Sakumudi, D.R., Watson, S.P.

(2014) Bioorg Med Chem Lett 24: 177-180

PubMed: 24355129 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2013.11.046
Primary Citation of Related Structures:
4N7E

PubMed Abstract:
The identification of the novel, selective, orally bioavailable Sortilin inhibitor AF38469 is described. Structure-activity relationships and syntheses are reported, along with an X-ray crystal structure of the sortilin-AF38469 protein-inhibitor complex.

Organizational Affiliation

Neuroscience Drug Discovery, H. Lundbeck A/S, Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 79.28 kDa
Atom Count: 5,291
Modelled Residue Count: 653
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortilin	A	696	Homo sapiens	Mutation(s): 1 Gene Names: SORT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99523 (Homo sapiens) Explore Q99523 Go to UniProtKB: Q99523
PHAROS: Q99523 GTEx: ENSG00000134243
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99523
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2JQ Query on 2JQ Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-[(6-methylpyridin-2-yl)carbamoyl]-5-(trifluoromethyl)benzoic acid C₁₅ H₁₁ F₃ N₂ O₃ JWCUSQCZMQIBMR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
2JQ	BindingDB: 4N7E	Ki: min: 210, max: 429 (nM) from 2 assay(s)
2JQ	BindingDB: 4N7E	IC50: min: 220, max: 1800 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.242
R-Value Work: 0.201
R-Value Observed: 0.204
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.948	α = 90
b = 77.402	β = 127.06
c = 111.176	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

Andersen, J.L.

Strandbygaard, D.

Thirup, S.

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary