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- PDB-8wuz: Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidi... -

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Basic information

Entry
Database: PDB / ID: 8wuz
TitleDevelopment of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / Mitochondria / Caseinolytic Protease P / activator / antitumor
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
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
BROMIDE ION / : / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJiang, J.-X. / Ding, H. / Chen, M.-R. / Lu, M.-L. / Sun, H.-Y. / Xiao, Y.-B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators
Authors: Jiang, J.-X. / Ding, H. / Chen, M.-R. / Lu, M.-L. / Sun, H.-Y. / Xiao, Y.-B.
History
DepositionOct 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,20622
Polymers169,2597
Non-polymers3,94715
Water00
1
A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules

A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,41144
Polymers338,51814
Non-polymers7,89330
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area55810 Å2
ΔGint-235 kcal/mol
Surface area89530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.277, 184.938, 163.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 24179.875 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical
ChemComp-XFU / 5-[(3-fluorophenyl)methyl]-9-[[4-(trifluoromethyl)phenyl]methyl]-1,5,9,11-tetrazatricyclo[8.4.0.0^{2,7}]tetradeca-2(7),10-dien-8-one


Mass: 472.478 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C25H24F4N4O
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
Has ligand of interestN
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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M NaBr, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→47.75 Å / Num. obs: 83250 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.995 / Net I/σ(I): 8.1
Reflection shellResolution: 2.9→2.9 Å / Num. unique obs: 6199 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
AUTOMARdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.75 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1979 3.97 %
Rwork0.2333 --
obs0.235 49874 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9882 0 246 0 10128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110329
X-RAY DIFFRACTIONf_angle_d1.24514021
X-RAY DIFFRACTIONf_dihedral_angle_d22.7933893
X-RAY DIFFRACTIONf_chiral_restr0.0671587
X-RAY DIFFRACTIONf_plane_restr0.0091749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.34681400.31043394X-RAY DIFFRACTION100
2.97-3.050.3341390.2783358X-RAY DIFFRACTION100
3.05-3.140.31551380.28283372X-RAY DIFFRACTION100
3.14-3.240.30681410.28253405X-RAY DIFFRACTION100
3.24-3.360.32241400.26873387X-RAY DIFFRACTION100
3.36-3.490.32611420.26083415X-RAY DIFFRACTION100
3.49-3.650.28861380.2353376X-RAY DIFFRACTION100
3.65-3.850.24741420.23553412X-RAY DIFFRACTION100
3.85-4.090.26271410.22443436X-RAY DIFFRACTION100
4.09-4.40.2331420.19573415X-RAY DIFFRACTION100
4.4-4.840.24831410.19813409X-RAY DIFFRACTION100
4.85-5.540.25091420.20913448X-RAY DIFFRACTION100
5.55-6.980.28171450.2263498X-RAY DIFFRACTION100
6.98-47.750.24211480.20853570X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.1516 Å / Origin y: -37.8464 Å / Origin z: -16.9009 Å
111213212223313233
T0.2421 Å20.0083 Å20.0031 Å2-0.1576 Å20.0118 Å2--0.1708 Å2
L0.3323 °2-0.0215 °2-0.0838 °2-0.2321 °2-0.0476 °2--0.9497 °2
S-0.0606 Å °-0.098 Å °-0.0494 Å °0.0454 Å °0.0035 Å °-0.0208 Å °0.1175 Å °0.013 Å °0.0502 Å °
Refinement TLS groupSelection details: all

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