4YVF | pdb_00004yvf

Structure of S-adenosyl-L-homocysteine hydrolase

• PDB DOI: https://doi.org/10.2210/pdb4YVF/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.239 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

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

• PubMed: 26037610 
• DOI: https://doi.org/10.1016/j.bmc.2015.05.018
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan. Electronic address: [e-mail].
Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 97.99 kDa 
• Atom Count: 7,052 
• Modeled Residue Count: 858 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B	432	Homo sapiens	Mutation(s): 0  Gene Names: AHCY, SAHH EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23526 (Homo sapiens) Explore P23526  Go to UniProtKB:  P23526
PHAROS:  P23526 GTEx:  ENSG00000101444

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A], E [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
XFA	D [auth A], F [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
XFA	BindingDB:  4YVF	Ki: 1.5 (nM) from 1 assay(s)
		IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.239 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.528	α = 90
b = 134.15	β = 90
c = 185.164	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references