4YVF

Structure of S-adenosyl-L-homocysteine hydrolase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  
    4YVF

  • 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 crystal structure of AdoHcyase with NAD(+) and 18a showed a novel open form co-crystal structure ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosylhomocysteinase A, B432Homo sapiensMutation(s): 0 
Gene Names: AHCY, SAHH
EC: 3.3.1.1
Find proteins for P23526 (Homo sapiens)
Explore P23526 
Go to UniProtKB:  P23526
NIH Common Fund Data Resources
PHAROS:  P23526
GTEx:  ENSG00000101444
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI
Download Ideal Coordinates CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N		 Ligand Interaction
XFA
Query on XFA
Download Ideal Coordinates 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.528α = 90
b = 134.15β = 90
c = 185.164γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Database references, Derived calculations