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- PDB-9uny: Natural product inhibitor of glyceraldehyde-3-phosphate dehydroge... -

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Basic information

Entry
Database: PDB / ID: 9uny
TitleNatural product inhibitor of glyceraldehyde-3-phosphate dehydrogenase(GAPDH)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Tetramer / Active catalytic site CYS152
Function / homology
Function and homology information


peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / : / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / canonical glycolysis ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / : / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / canonical glycolysis / negative regulation of formation of translation preinitiation complex / GAIT complex / peptidyl-cysteine S-nitrosylase activity / defense response to fungus / neuron apoptotic process / regulation of macroautophagy / positive regulation of type I interferon production / glycolytic process / positive regulation of cytokine production / lipid droplet / cellular response to type II interferon / microtubule cytoskeleton organization / NAD binding / disordered domain specific binding / microtubule cytoskeleton / NADP binding / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / microtubule binding / vesicle / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / negative regulation of translation / ribonucleoprotein complex / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / FORMAMIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsFu, Q. / Xiao, Q.-Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Phytomedicine / Year: 2026
Title: GAPDH inhibition by oridonin integrates glycolytic inhibition and anti-inflammation to alleviate rheumatoid arthritis synovitis.
Authors: Xiao, Q. / Zhou, H. / Li, M. / Peng, Y. / Huang, Y. / Zhao, Y. / Chen, S. / Chen, H. / Zhang, C. / Yuan, Q. / Qiu, L. / He, Y. / Dai, Z. / Peng, T. / Fu, Q.
History
DepositionApr 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Glyceraldehyde-3-phosphate dehydrogenase
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,41841
Polymers144,3974
Non-polymers3,02137
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23090 Å2
ΔGint-87 kcal/mol
Surface area43450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.235, 125.934, 132.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules PABC

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / Peptidyl-cysteine S-nitrosylase GAPDH


Mass: 36099.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups

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Non-polymers , 6 types, 238 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: CH3NO
#4: Chemical ChemComp-A1EP4 / (1~{S},2~{S},5~{S},6~{S},8~{R},9~{S},10~{S},11~{R},15~{S},18~{R})-6,12,12-trimethyl-9,10,15,18-tetrakis(oxidanyl)-17-oxapentacyclo[7.6.2.1^{5,8}.0^{1,11}.0^{2,8}]octadecan-7-one


Mass: 366.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O6
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium acetate, 0.1M HEPES-NaOH pH7.5, 22%(W/V) PEG4000, 4.4%(V/V) Formamide

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Mar 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→62.967 Å / Num. obs: 85324 / % possible obs: 99.4 % / Redundancy: 10.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.253 / Net I/σ(I): 2.77
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID% possible allRrim(I) all
4.03-5.0778030.9981100
3.29-4.0399820.9951100
2.85-3.29117070.986199.9
2.55-2.85131750.938199.9
2.33-2.55139480.789198.9
2.15-2.33101410.433191.9
2.01-2.1572800.121183.1
1.9-2.0122540.05174.2
1.8-1.91789164.727.25

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8F

1u8f


Resolution: 1.87→62.967 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 1864 2.62 %
Rwork0.2119 --
obs0.2137 71022 60.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→62.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10293 0 1 201 10495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01510492
X-RAY DIFFRACTIONf_angle_d1.34514183
X-RAY DIFFRACTIONf_dihedral_angle_d14.4926174
X-RAY DIFFRACTIONf_chiral_restr0.0661602
X-RAY DIFFRACTIONf_plane_restr0.0091819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8702-1.92070.927760.8807285X-RAY DIFFRACTION3
1.9207-1.97730.876450.8322194X-RAY DIFFRACTION2
1.9773-2.04110.5517130.392533X-RAY DIFFRACTION7
2.0411-2.1140.461450.41221537X-RAY DIFFRACTION18
2.114-2.19870.4628880.38433327X-RAY DIFFRACTION38
2.1987-2.29880.39981100.35834526X-RAY DIFFRACTION52
2.2988-2.41990.33911620.32396000X-RAY DIFFRACTION68
2.4199-2.57160.35952270.28558215X-RAY DIFFRACTION94
2.5716-2.77010.3412340.2698772X-RAY DIFFRACTION100
2.7701-3.04890.32592410.24298808X-RAY DIFFRACTION100
3.0489-3.490.29292400.20098828X-RAY DIFFRACTION100
3.49-4.39690.22172430.14568905X-RAY DIFFRACTION100
4.3969-62.9670.19422500.13579228X-RAY DIFFRACTION100

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