4YVF

Structure of S-adenosyl-L-homocysteine hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery and structural analyses of S-adenosyl-L-homocysteine hydrolase inhibitors based on non-adenosine analogs.

Nakao, A.Suzuki, H.Ueno, H.Iwasaki, H.Setsuta, T.Kashima, A.Sunada, S.

(2015) Bioorg.Med.Chem. 23: 4952-4969

  • DOI: 10.1016/j.bmc.2015.05.018

  • PubMed Abstract: 
  • Optimization of a new series of S-adenosyl-L-homocysteine hydrolase (AdoHcyase) inhibitors based on non-adenosine analogs led to very potent compounds 14n, 18a, and 18b with IC50 values of 13 ± 3, 5.0 ± 2.0, and 8.5 ± 3.1 nM, respectively. An X-ray c ...

    Optimization of a new series of S-adenosyl-L-homocysteine hydrolase (AdoHcyase) inhibitors based on non-adenosine analogs led to very potent compounds 14n, 18a, and 18b with IC50 values of 13 ± 3, 5.0 ± 2.0, and 8.5 ± 3.1 nM, respectively. An X-ray crystal structure of AdoHcyase with NAD(+) and 18a showed a novel open form co-crystal structure. 18a in the co-crystals formed intramolecular eight membered ring hydrogen bond formations. A single crystal X-ray structure of 14n also showed an intramolecular eight-membered ring hydrogen bond interaction.


    Organizational Affiliation

    Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan. Electronic address: Nakao.Akira@mc.mt-pharma.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosylhomocysteinase
A, B
432Homo sapiensGene Names: AHCY (SAHH)
EC: 3.3.1.1
Find proteins for P23526 (Homo sapiens)
Go to Gene View: AHCY
Go to UniProtKB:  P23526
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XFA
Query on XFA

Download SDF File 
Download CCD File 
A, B
2-{[5-chloro-2-(4-chlorophenoxy)phenyl](2-{[2-(methylamino)ethyl]amino}-2-oxoethyl)amino}-N-(1,3-dihydro-2H-isoindol-2-yl)-N-methylacetamide
C28 H31 Cl2 N5 O3
AOQCCSFIEWPXMC-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 91.528α = 90.00
b = 134.150β = 90.00
c = 185.164γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data scaling
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-03-20 
  • Released Date: 2015-11-25 
  • Deposition Author(s): Akiko, K.

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release