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- PDB-11op: Crystal Structure of M. tuberculosis ClpP1P2 bound to ONC201 -

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Basic information

Entry
Database: PDB / ID: 11op
TitleCrystal Structure of M. tuberculosis ClpP1P2 bound to ONC201
Components(ATP-dependent Clp protease proteolytic subunit ...) x 2
KeywordsANTIBIOTIC / peptidase / protease / mycobacteria / tuberculosis / acyldepsipeptide / proteostasis
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / 2-(2-ETHOXYETHOXY)ETHANOL / BENZOIC ACID / LEUCINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsBurnside, C.M. / Fei, F. / Schmitz, K.R. / Sello, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI171196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM133395 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI123400 United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structural and Mechanistic Studies of ADEPs Yield Potent Antibacterials and a Drug Formulation Strategy for Tuberculosis.
Authors: Fei, F. / Burnside, C.M. / Lun, S. / Wee, D. / Kaur, M. / Anderson, H.R. / McCarroll, M.N. / Richardson, A.E. / Neglia, S. / Liu, H.M. / Wang, X. / Gupta, S. / Rhee, K.Y. / Wright, G.D. / ...Authors: Fei, F. / Burnside, C.M. / Lun, S. / Wee, D. / Kaur, M. / Anderson, H.R. / McCarroll, M.N. / Richardson, A.E. / Neglia, S. / Liu, H.M. / Wang, X. / Gupta, S. / Rhee, K.Y. / Wright, G.D. / Bryson, B.D. / Oehlers, S.H. / Bishai, W.R. / Schmitz, K.R. / Sello, J.K.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,62663
Polymers313,01814
Non-polymers9,60849
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62780 Å2
ΔGint-187 kcal/mol
Surface area89580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.268, 181.830, 95.133
Angle α, β, γ (deg.)90.000, 94.715, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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ATP-dependent Clp protease proteolytic subunit ... , 2 types, 14 molecules ABCDEFGHIJKLMN

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 23650.910 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: mature M. tuberculosis ClpP2 with a C-terminal 6xHis tag
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: clpP2, Rv2460c, MTV008.16c / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / Variant (production host): delta-clpP / References: UniProt: P9WPC3, endopeptidase Clp
#2: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 21065.934 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: mature M. tuberculosis ClpP1
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: clpP1, clpP, Rv2461c, MTV008.17c / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / Variant (production host): delta-clpP / References: UniProt: P9WPC5, endopeptidase Clp

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Non-polymers , 10 types, 123 molecules

#3: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical
ChemComp-A1C98 / Dordaviprone / (10R)-7-benzyl-4-[(2-methylphenyl)methyl]-2,4,6,7,8,9-hexahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(1H)-one / ONC201


Mass: 386.489 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H26N4O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.9 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz- ...Details: 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz-Leu-Leu, 10 mM HEPES (pH 7.5), 50 mM NaCl, 4.5% DMSO)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2022
Details: horizontal bounce Si(111) double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 62136 / % possible obs: 98.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 75.04 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.099 / Rrim(I) all: 0.181 / Net I/σ(I): 8.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
8.4-500.03130.3331410.9980.9990.020.037
6.67-8.43.50.0526.731600.9960.9990.0310.05999.5
5.83-6.673.70.08414.731610.9920.9980.050.09899.7
5.3-5.833.80.09813.731550.9910.9980.0580.11499.6
4.92-5.33.70.09911.531440.9910.9980.0590.11699.4
4.63-4.9230.091130220.990.9970.0580.10895.4
4.4-4.6330.09611.430770.9910.9980.0650.11797
4.21-4.430.1221030970.9840.9960.0770.14598.6
4.04-4.213.50.1528.631540.9770.9940.0930.17999.2
3.91-4.043.40.196731060.9650.9910.1210.23199
3.78-3.9130.2065.3331200.9460.9860.1380.2598.7
3.68-3.782.90.2613.7131260.9050.9750.1820.32199
3.58-3.682.90.2913.4331250.8880.970.2030.35799
3.49-3.5830.3383.2931060.890.970.2280.40998.5
3.41-3.5830.4352.5731510.8140.9470.2920.52699
3.34-3.4130.4852.13130710.7790.9360.3290.58998.4
3.27-3.342.90.5761.8830700.7060.910.3960.70397.9
3.21-3.272.90.611.6330670.6720.8960.4190.74496.8
3.15-3.212.80.6911.530360.6070.8690.4770.84496.5
3.1-3.152.70.929130470.470.80.6651.14996.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→31.59 Å / SU ML: 0.4254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2417 2778 5.03 %
Rwork0.1867 52474 -
obs0.1895 55252 86.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.67 Å2
Refinement stepCycle: LAST / Resolution: 3.11→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19972 0 673 74 20719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007220989
X-RAY DIFFRACTIONf_angle_d0.937928399
X-RAY DIFFRACTIONf_chiral_restr0.05813226
X-RAY DIFFRACTIONf_plane_restr0.00783637
X-RAY DIFFRACTIONf_dihedral_angle_d14.27287610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.170.49540.34531028X-RAY DIFFRACTION33.53
3.17-3.220.3961780.28321380X-RAY DIFFRACTION46.57
3.22-3.290.3113950.2841788X-RAY DIFFRACTION58.77
3.29-3.350.33211230.27552195X-RAY DIFFRACTION73.7
3.35-3.430.33371370.27012542X-RAY DIFFRACTION84.32
3.43-3.510.31891540.26682778X-RAY DIFFRACTION92.23
3.51-3.590.35981440.25152775X-RAY DIFFRACTION92.55
3.59-3.690.30291520.2362887X-RAY DIFFRACTION95.39
3.69-3.80.2991550.21752910X-RAY DIFFRACTION95.69
3.8-3.920.28951510.2072861X-RAY DIFFRACTION95.89
3.92-4.060.2691580.19772916X-RAY DIFFRACTION96.27
4.06-4.220.21971420.17742946X-RAY DIFFRACTION96.8
4.22-4.410.22461590.15892881X-RAY DIFFRACTION96.11
4.42-4.650.18931430.15782891X-RAY DIFFRACTION95.2
4.65-4.940.19851580.15512806X-RAY DIFFRACTION93.41
4.94-5.320.20251520.16112967X-RAY DIFFRACTION97.47
5.32-5.850.20581530.17842966X-RAY DIFFRACTION97.62
5.85-6.690.24331580.17932974X-RAY DIFFRACTION98.21
6.69-8.40.20981510.15332991X-RAY DIFFRACTION98.28
8.4-31.590.17831610.14342992X-RAY DIFFRACTION96.81

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