4GR9

Synthesis of novel MT3 receptor ligands via unusual Knoevenagel condensation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.291 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2012.10.005
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Moscow State University, Chemistry department, Leninskie Gory 1, Moscow, Russia. maria.s.volkov@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosyldihydronicotinamide dehydrogenase [quinone]
A, B
230Homo sapiensMutation(s): 0 
Gene Names: NQO2 (NMOR2)
EC: 1.10.5.1
Find proteins for P16083 (Homo sapiens)
Go to Gene View: NQO2
Go to UniProtKB:  P16083
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
372
Query on 372

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Download CCD File 
A, B
N-[(3R)-3-(cyanomethyl)-1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl]acetamide
C13 H13 N3 O2
PFJVUECMVVMLTI-SNVBAGLBSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
372IC50: 7000 nM (99) BINDINGDB
372IC50: 7000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.291 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.609α = 90.00
b = 83.369β = 90.00
c = 106.494γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description