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- PDB-11li: OgOGA IN COMPLEX WITH LIGAND 24 -

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Basic information

Entry
Database: PDB / ID: 11li
TitleOgOGA IN COMPLEX WITH LIGAND 24
ComponentsProtein O-GlcNAcase
KeywordsHYDROLASE/INHIBITOR / GLYCOSIDE HYDROLASE / INHIBITOR / HYDROLASE / HYDROLASE-INHIBITOR Complex
Function / homology
Function and homology information


protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Protein O-GlcNAcase
Similarity search - Component
Biological speciesOceanicola granulosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsShaffer, P.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Discovery of 5‐Azaindole Inhibitors of O‐GlcNAcase for the Treatment of Alzheimer's Disease and Related Tauopathies.
Authors: Bouton, J. / Bretteville, A. / Tresadern, G. / Shaffer, P. / Austin, N. / Buijnsters, P. / Cedervall, E.P. / Darville, N. / Fonteyn, I. / Leenaerts, J. / Lamenca, C.M. / Mertens, L. / ...Authors: Bouton, J. / Bretteville, A. / Tresadern, G. / Shaffer, P. / Austin, N. / Buijnsters, P. / Cedervall, E.P. / Darville, N. / Fonteyn, I. / Leenaerts, J. / Lamenca, C.M. / Mertens, L. / Peeters, D. / Velter, A.I. / Roosbroeck, Y.V. / Ebneth, A. / Bartolome, J.M. / Trabanco, A.A. / Oehlrich, D.
History
DepositionMar 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2298
Polymers50,2431
Non-polymers9877
Water6,071337
1
A: Protein O-GlcNAcase
hetero molecules

A: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,45916
Polymers100,4852
Non-polymers1,97314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)84.634, 93.038, 60.394
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-615-

HOH

21A-890-

HOH

31A-905-

HOH

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Components

#1: Protein Protein O-GlcNAcase / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / N-acetyl- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase


Mass: 50242.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanicola granulosus (bacteria) / Strain: HTCC2516 / Gene: OG2516_04129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2CEE3, protein O-GlcNAcase
#2: Chemical ChemComp-A1DE3 / N,N-dimethyl-2-(4-{[4-methyl-2-(propan-2-yl)pyridin-3-yl]amino}-1H-pyrrolo[3,2-c]pyridin-1-yl)acetamide


Mass: 351.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.25
Details: 16% (w/v) PEG4K, 0.15 M MgCl2, 0.1M Tris/HCl pH 8.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→61.56 Å / Num. obs: 65376 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.055 / Net I/σ(I): 15.19
Reflection shellResolution: 1.53→1.78 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 24368 / CC1/2: 0.885 / Rrim(I) all: 0.605 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→61.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.402 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22737 4032 6.2 %RANDOM
Rwork0.1891 ---
obs0.19146 61188 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å21.14 Å2
2--0.51 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.53→61.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 69 337 3876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193682
X-RAY DIFFRACTIONr_bond_other_d0.0050.023454
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9645032
X-RAY DIFFRACTIONr_angle_other_deg1.40137879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07222.179179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.251541
X-RAY DIFFRACTIONr_chiral_restr0.1260.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214259
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02914
X-RAY DIFFRACTIONr_mcbond_other2.4522.0041784
X-RAY DIFFRACTIONr_mcangle_it3.253.3742236
X-RAY DIFFRACTIONr_mcangle_other3.253.3782237
X-RAY DIFFRACTIONr_scbond_it3.8192.461897
X-RAY DIFFRACTIONr_scbond_other3.812.461897
X-RAY DIFFRACTIONr_scangle_other4.9873.9712791
X-RAY DIFFRACTIONr_long_range_B_refined6.56719.9964277
X-RAY DIFFRACTIONr_long_range_B_other6.49419.394209
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.567 287 -
Rwork0.502 4521 -
obs--94.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5555-0.00590.24090.6131-0.19581.9043-0.0809-0.2297-0.1610.0652-0.0001-0.02230.14420.26350.0810.03460.0530.01730.12370.03890.024515.3758.96229.588
22.0585-1.1547-0.23252.378-0.85141.45660.01060.17690.2380.11790.0458-0.0354-0.2489-0.276-0.05640.05160.02810.00550.14740.01540.0349-11.46825.75710.905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 294
2X-RAY DIFFRACTION2A295 - 447

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