6TOD | pdb_00006tod

Crystal structure of the Orexin-1 receptor in complex with EMPA

PDB DOI: https://doi.org/10.2210/pdb6TOD/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2019-12-11 Released: 2020-01-01
Deposition Author(s): Rappas, M., Ali, A., Bennett, K.A., Brown, J.D., Bucknell, S.J., Congreve, M., Cooke, R.M., Cseke, G., de Graaf, C., Dore, A.S., Errey, J.C., Jazayeri, A., Marshall, F.H., Mason, J.S., Mould, R., Patel, J.C., Tehan, B.G., Weir, M., Christopher, J.A.
Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.208 (Depositor)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis.

Rappas, M., Ali, A.A.E., Bennett, K.A., Brown, J.D., Bucknell, S.J., Congreve, M., Cooke, R.M., Cseke, G., de Graaf, C., Dore, A.S., Errey, J.C., Jazayeri, A., Marshall, F.H., Mason, J.S., Mould, R., Patel, J.C., Tehan, B.G., Weir, M., Christopher, J.A.

(2020) J Med Chem 63: 1528-1543

PubMed: 31860301 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.9b01787
Primary Citation Related Structures:
6TO7, 6TOD, 6TOS, 6TOT, 6TP3, 6TP4, 6TP6, 6TPG, 6TPJ, 6TPN, 6TQ4, 6TQ6, 6TQ7, 6TQ9

PubMed Abstract:
The orexin system, which consists of the two G protein-coupled receptors OX ₁ and OX ₂, activated by the neuropeptides OX-A and OX-B, is firmly established as a key regulator of behavioral arousal, sleep, and wakefulness and has been an area of intense research effort over the past two decades. X-ray structures of the receptors in complex with 10 new antagonist ligands from diverse chemotypes are presented, which complement the existing structural information for the system and highlight the critical importance of lipophilic hotspots and water molecules for these peptidergic GPCR targets. Learnings from the structural information regarding the utility of pharmacophore models and how selectivity between OX ₁ and OX ₂ can be achieved are discussed.

Organizational Affiliation

Sosei Heptares , Steinmetz Building, Granta Park , Cambridge CB21 6DG , U.K.

Macromolecule Content

Total Structure Weight: 94.73 kDa
Atom Count: 5,949
Modeled Residue Count: 612
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orexin receptor type 1	A, B	336	Homo sapiens	Mutation(s): 12 Gene Names: HCRTR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O43613 (Homo sapiens) Explore O43613 Go to UniProtKB: O43613
PHAROS: O43613 GTEx: ENSG00000121764
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43613
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download:Ideal Coordinates CCD File SDF format, chain KB [auth B] SDF format, chain EA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain EA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain EA [auth A]	EA [auth A], KB [auth B]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain EA [auth A] Focus chain KB [auth B] Interactions & Density Focus chain EA [auth A] Focus chain KB [auth B]
7MA (Subject of Investigation/LOI) Query on 7MA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain GA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain GA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain GA [auth B]	C [auth A], GA [auth B]	N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide C₂₃ H₂₆ N₄ O₄ S KJPHTXTWFHVJIG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain GA [auth B] Interactions & Density Focus chain C [auth A] Focus chain GA [auth B]
SOG Query on SOG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain FB [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain XA [auth B] SDF format, chain UA [auth B] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain QA [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain GB [auth B] SDF format, chain EB [auth B] SDF format, chain DB [auth B] SDF format, chain CB [auth B] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain BA [auth A]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth B], I [auth A], IB [auth B], J [auth A], JB [auth B], K [auth A], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	octyl 1-thio-beta-D-glucopyranoside C₁₄ H₂₈ O₅ S CGVLVOOFCGWBCS-RGDJUOJXSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], G [auth A], JA [auth B], KA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain KA [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain HA [auth B] SDF format, chain IA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B]	D [auth A], HA [auth B], IA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Interactions & Density Focus chain D [auth A] Focus chain HA [auth B] Focus chain IA [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain LB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain LB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain LB [auth B]	FA [auth A], LB [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain LB [auth B] Interactions & Density Focus chain FA [auth A] Focus chain LB [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
7MA	BindingDB: 6TOD	Ki: min: 900, max: 4467 (nM) from 3 assay(s)
7MA	BindingDB: 6TOD	IC50: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.208 (Depositor)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.189 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.907	α = 90
b = 158.891	β = 95.77
c = 182.354	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R01DA039553

Revision History (Full details and data files)

Version 1.0: 2020-01-01
Type: Initial release
Version 1.1: 2020-01-29
Changes: Database references
Version 1.2: 2020-03-11
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Structure summary
Version 1.4: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-10-23
Changes: Structure summary