6JKH

The NAD+-bound form of human NSDHL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of human NSDHL and development of its novel inhibitor with the potential to suppress EGFR activity.

Kim, D.G.Cho, S.Lee, K.Y.Cheon, S.H.Yoon, H.J.Lee, J.Y.Kim, D.Shin, K.S.Koh, C.H.Koo, J.S.Choi, Y.Lee, H.H.Oh, Y.K.Jeong, Y.S.Chung, S.J.Baek, M.Jung, K.Y.Lim, H.J.Kim, H.S.Park, S.J.Lee, J.Y.Lee, S.J.Lee, B.J.

(2021) Cell Mol Life Sci 78: 207-225

  • DOI: 10.1007/s00018-020-03490-2
  • Primary Citation of Related Structures:  
    6JKH, 6JKG

  • PubMed Abstract: 
  • NAD(P)-dependent steroid dehydrogenase-like (NSDHL), an essential enzyme in human cholesterol synthesis and a regulator of epidermal growth factor receptor (EGFR) trafficking pathways, has attracted interest as a therapeutic target due to its crucial relevance to cholesterol-related diseases and carcinomas ...

    NAD(P)-dependent steroid dehydrogenase-like (NSDHL), an essential enzyme in human cholesterol synthesis and a regulator of epidermal growth factor receptor (EGFR) trafficking pathways, has attracted interest as a therapeutic target due to its crucial relevance to cholesterol-related diseases and carcinomas. However, the development of pharmacological agents for targeting NSDHL has been hindered by the absence of the atomic details of NSDHL. In this study, we reported two X-ray crystal structures of human NSDHL, which revealed a detailed description of the coenzyme-binding site and the unique conformational change upon the binding of a coenzyme. A structure-based virtual screening and biochemical evaluation were performed and identified a novel inhibitor for NSDHL harboring suppressive activity towards EGFR. In EGFR-driven human cancer cells, treatment with the potent NSDHL inhibitor enhanced the antitumor effect of an EGFR kinase inhibitor. Overall, these findings could serve as good platforms for the development of therapeutic agents against NSDHL-related diseases.


    Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea. lbj@nmr.snu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylatingA, B245Homo sapiensMutation(s): 0 
Gene Names: NSDHLH105E3
EC: 1.1.1.170
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15738 (Homo sapiens)
Explore Q15738 
Go to UniProtKB:  Q15738
PHAROS:  Q15738
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.027α = 90
b = 77.366β = 96.8
c = 53.993γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1C1B2014609
National Research Foundation (Korea)Korea, Republic OfNRF-2018R1A2A1A19018526
National Research Foundation (Korea)Korea, Republic OfNRF-2018R1A5A2024425

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references, Structure summary