5TIO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine receptor subunit alpha-3A [auth C],
B [auth A],
C [auth B],
D,
E
362Homo sapiensMutation(s): 0 
Gene Names: GLRA3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75311 (Homo sapiens)
Explore O75311 
Go to UniProtKB:  O75311
PHAROS:  O75311
GTEx:  ENSG00000145451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75311
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O75311-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7C6
Query on 7C6

Download Ideal Coordinates CCD File 
F [auth C],
J [auth A],
M [auth B],
P [auth D],
S [auth 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
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
G [auth C],
K [auth A],
N [auth B],
R [auth D],
T [auth E]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth C],
L [auth A],
O [auth B],
Q [auth D],
U [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7C6 BindingDB:  5TIO Kd: 11 (nM) from 1 assay(s)
EC50: min: 16, max: 50 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.12α = 90
b = 119.12β = 90
c = 429.968γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary