9DMU | pdb_00009dmu

Cryo-EM structure of IMPDH2 bound to IMP and GAD

PDB DOI: https://doi.org/10.2210/pdb9DMU/pdb
EM Map EMD-47016: EMDB EMDataResource

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

Deposited: 2024-09-14 Released: 2024-11-27
Deposition Author(s): Chen, Y.J., Li, B., Parada, L.F.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

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

Starting Model: experimental
View more details

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

PubMed: 39567689 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-024-08224-z
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 458.94 kDa
Atom Count: 24,084
Modeled Residue Count: 3,032
Deposited Residue Count: 4,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase 2	A, B, C, D, E A, B, C, D, E, F, G, H	518	Homo sapiens	Mutation(s): 0 Gene Names: IMPDH2, IMPD2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12268
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A7T (Subject of Investigation/LOI) Query on A1A7T Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain FA [auth H] SDF format, chain BA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain BA [auth G]	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		Interactions Focus chain BA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth F]
IMP Query on IMP Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain EA [auth H] SDF format, chain AA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain AA [auth G]	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		Interactions Focus chain AA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain X [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain DA [auth H] SDF format, chain CA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth G]	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		Interactions Focus chain CA [auth G] Focus chain DA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain DA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Chen, Y.J.

Li, B.

Parada, L.F.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA210100
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA196519-01
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA008748