9DMU | pdb_00009dmu

Cryo-EM structure of IMPDH2 bound to IMP and GAD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma.

Chen, Y.J.Iyer, S.V.Hsieh, D.C.Li, B.Elias, H.K.Wang, T.Li, J.Ganbold, M.Lien, M.C.Peng, Y.C.Xie, X.P.Jayewickreme, C.D.van den Brink, M.R.M.Brady, S.F.Lim, S.K.Parada, L.F.

(2024) Nature 636: 466-473

  • DOI: https://doi.org/10.1038/s41586-024-08224-z
  • Primary Citation of Related Structures:  
    9DMU

  • PubMed Abstract: 

    Glioblastoma is incurable and in urgent need of improved therapeutics 1 . Here we identify a small compound, gliocidin, that kills glioblastoma cells while sparing non-tumour replicative cells. Gliocidin activity targets a de novo purine synthesis vulnerability in glioblastoma through indirect inhibition of inosine monophosphate dehydrogenase 2 (IMPDH2). IMPDH2 blockade reduces intracellular guanine nucleotide levels, causing nucleotide imbalance, replication stress and tumour cell death 2 . Gliocidin is a prodrug that is anabolized into its tumoricidal metabolite, gliocidin-adenine dinucleotide (GAD), by the enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) of the NAD + salvage pathway. The cryo-electron microscopy structure of GAD together with IMPDH2 demonstrates its entry, deformation and blockade of the NAD + pocket 3 . In vivo, gliocidin penetrates the blood-brain barrier and extends the survival of mice with orthotopic glioblastoma. The DNA alkylating agent temozolomide induces Nmnat1 expression, causing synergistic tumour cell killing and additional survival benefit in orthotopic patient-derived xenograft models. This study brings gliocidin to light as a prodrug with the potential to improve the survival of patients with glioblastoma.


  • Organizational Affiliation
    • Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase 2
A, B, C, D, E
A, B, C, D, E, F, G, H
518Homo sapiensMutation(s): 0 
Gene Names: IMPDH2IMPD2
EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens)
Explore P12268 
Go to UniProtKB:  P12268
PHAROS:  P12268
GTEx:  ENSG00000178035 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12268
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A7T (Subject of Investigation/LOI)
Query on A1A7T

Download Ideal Coordinates CCD File 
BA [auth G]
FA [auth H]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
FA [auth H],
J [auth A],
M [auth B],
P [auth C],
T [auth D],
V [auth E],
Y [auth F]
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[3-(thiophen-2-ylcarbonylamino)pyridin-1-yl]oxolan-2-yl]methyl hydrogen phosphate
C25 H30 N7 O14 P2 S
DPLWQOAIFYMWQG-DLOVRGRYSA-O
IMP
Query on IMP

Download Ideal Coordinates CCD File 
AA [auth G]
EA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
EA [auth H],
I [auth A],
L [auth B],
O [auth C],
S [auth D],
U [auth E],
X [auth F]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CA [auth G]
DA [auth H]
K [auth A]
N [auth B]
Q [auth C]
CA [auth G],
DA [auth H],
K [auth A],
N [auth B],
Q [auth C],
R [auth D],
W [auth E],
Z [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA210100
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA196519-01
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA008748

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-12-25
    Changes: Data collection, Database references