4GR9

Synthesis of novel MT3 receptor ligands via unusual Knoevenagel condensation

• PDB DOI: https://doi.org/10.2210/pdb4GR9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-24 Released: 2013-07-10 
• Deposition Author(s): Volkova, M.S., Jensen, K.C., Lozinskaya, N.A., Sosonyuk, S.E., Proskurnina, M.V., Mesecar, A.D., Zefirov, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.232 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Literature

Synthesis of novel МТ3 receptor ligands via an unusual Knoevenagel condensation.

Volkova, M.S., Jensen, K.C., Lozinskaya, N.A., Sosonyuk, S.E., Proskurnina, M.V., Mesecar, A.D., Zefirov, N.S.

(2012) Bioorg Med Chem Lett 22: 7578-7581

• PubMed: 23131339 
• DOI: https://doi.org/10.1016/j.bmcl.2012.10.005
• Primary Citation of Related Structures:  
  4GQI, 4GR9


• PubMed Abstract: 
  

  New 5-acetamido-substituted melatonin derivatives were efficiently synthesized in excellent yields via Knoevenagel condensation. The relative binding affinity of new synthesized compounds to MT3 receptor was tested via enzymatic assays and the X-ray structures of the most potent compounds were determined in complex with MT3.

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Organizational Affiliation: 

Moscow State University, Chemistry department, Leninskie Gory 1, Moscow, Russia. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.98 kDa 
• Atom Count: 4,023 
• Modelled Residue Count: 460 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B	230	Homo sapiens	Mutation(s): 0  Gene Names: NQO2, NMOR2 EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens) Explore P16083  Go to UniProtKB:  P16083
PHAROS:  P16083 GTEx:  ENSG00000124588

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
372	E [auth A], I [auth B]	N-[(3R)-3-(cyanomethyl)-1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl]acetamide C13 H13 N3 O2 PFJVUECMVVMLTI-SNVBAGLBSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
372	BindingDB:  4GR9	IC50: 7000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.232 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.609	α = 90
b = 83.369	β = 90
c = 106.494	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Volkova, M.S., Jensen, K.C., Lozinskaya, N.A., Sosonyuk, S.E., Proskurnina, M.V., Mesecar, A.D., Zefirov, N.S.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations