1U7T | pdb_00001u7t

Crystal Structure of ABAD/HSD10 with a Bound Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1U7T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-08-04 Released: 2004-10-05 
• Deposition Author(s): Kissinger, C.R., Rejto, P.A., Pelletier, L.A., Showalter, R.E., Villafranca, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human ABAD/HSD10 with a bound inhibitor: implications for design of Alzheimer's disease therapeutics

Kissinger, C.R., Rejto, P.A., Pelletier, L.A., Thomson, J.A., Showalter, R.E., Abreo, M.A., Agree, C.S., Margosiak, S., Meng, J.J., Aust, R.M., Vanderpool, D., Li, B., Tempczyk-Russell, A., Villafranca, J.E.

(2004) J Mol Biology 342: 943-952

• PubMed: 15342248 
• DOI: https://doi.org/10.1016/j.jmb.2004.07.071
• Primary Citation Related Structures: 
  1U7T


• PubMed Abstract: 
  

  The enzyme 17beta-hydroxysteroid dehydrogenase type 10 (HSD10), also known as amyloid beta-peptide-binding alcohol dehydrogenase (ABAD), has been implicated in the development of Alzheimer's disease. This protein, a member of the short-chain dehydrogenase/reductase family of enzymes, has been shown to bind beta-amyloid and to participate in beta-amyloid neurotoxicity. We have determined the crystal structure of human ABAD/HSD10 complexed with NAD(+) and an inhibitory small molecule. The inhibitor occupies the substrate-binding site and forms a covalent adduct with the NAD(+) cofactor. The crystal structure provides a basis for the design of potent, highly specific ABAD/HSD10 inhibitors with potential application in the treatment of Alzheimer's disease.

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Organizational Affiliation: 
• Pfizer-La Jolla, 10777 Science Center Dr., San Diego, CA 92121, USA.

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: 111.75 kDa 
• Atom Count: 7,760 
• Modeled Residue Count: 1,020 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase type II	A, B, C, D	261	Homo sapiens	Mutation(s): 1  Gene Names: HADH2, ERAB, XH98G2, SCHAD EC: 1.1.1.35 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1.178 (UniProt), 1.1.1.239 (UniProt), 1.1.1.159 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99714 (Homo sapiens) Explore Q99714  Go to UniProtKB:  Q99714
PHAROS:  Q99714 GTEx:  ENSG00000072506

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TDT	E [auth A], G [auth C], H [auth D]	1-AZEPAN-1-YL-2-PHENYL-2-(4-THIOXO-1,4-DIHYDRO-PYRAZOLO[3,4-D]PYRIMIDIN-5-YL)ETHANONE ADDUCT C40 H44 N12 O15 P2 S XHBACRZQFHLVAV-LFFSAXSQSA-L
NAD	F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.215 (Depositor) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122	α = 90
b = 80.8	β = 105.6
c = 110	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Kissinger, C.R., Rejto, P.A., Pelletier, L.A., Showalter, R.E., Villafranca, J.E.

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection
• Version 1.6: 2024-04-03
  Changes: Refinement description