Crystal Structures of Human GlyRa3 Bound to a Novel Class of Potentiators with Efficacy in a Mouse Model of Neuropathic Pain

Huang, X; Shaffer, P.L; Ayube, S; Bregman, H; Chen, H; Lehto, S.G; Luther, J.A; Matson, D.J; McDonough, S.I; Michelsen, K; Plant, M.M; Schneider, S; Simard, J.R; Teffera, Y; Yi, S; Zhang, M; DiMauro, E.F; Gingras, J.

doi:10.2210/pdb5tin/pdb

Macromolecule Content

Unique protein chains: 1

5TIN

Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607

DOI: 10.2210/pdb5tin/pdb

Classification: TRANSPORT PROTEIN
Deposited: 2016-10-03 Released: 2017-01-18
Deposition author(s): Shaffer, P.L., Huang, X., Chen, H.
Organism: Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): 1

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.214
R-Value Work: 0.204

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: TRANSPORT PROTEIN

Total Structure Weight: 212102.14

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Glycine receptor subunit alpha-3	A, B, C, D, E	362	Homo sapiens	Fragment: UNP residues 34-460, with 343-418 deleted Mutation: N38Q Gene Name(s): GLRA3 Gene View
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: O75311 UniProt Full Protein Feature View for O75311 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for O75311/5TIN

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Cys-Loop Receptor Family

Protein Name: α1 GlyR Glycine receptor in complex with strychnine

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
7C6 Query on 7C6 Download SDF File Download CCD File	A, B, C, D, E	(3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]- 3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4- c][1,6]naphthyridin-4-one C₁₉ H₁₉ N₃ O₅ S MXNQASHPCAMJHG-UCMVZMLTSA-N	Poseview Image of 7C6 in 5TIN Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
GLY Query on GLY Download SDF File Download CCD File	A, B, C, D, E	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N	Poseview Image of GLY in 5TIN Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
ZN Query on ZN Download SDF File Download CCD File	A, B, C, D, E	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N	Poseview Image of ZN in 5TIN Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CL Query on CL Download SDF File Download CCD File	E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 5TIN Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)