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- PDB-7r2j: Human Cyclophilin D in complex with N-(4-aminophenyl)-7-methyl-2-... -

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Basic information

Entry
Database: PDB / ID: 7r2j
TitleHuman Cyclophilin D in complex with N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Cyclophilin D PPIase
Function / homology
Function and homology information


: / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding ...: / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / necroptotic process / negative regulation of intrinsic apoptotic signaling pathway / apoptotic mitochondrial changes / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-V0Z / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsSilva, D.O. / Graedler, U. / Bandeiras, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structure-based design of pyrazole derivatives targeting the human Cyclophilin D binding site
Authors: Silva, D.O. / Freitas, M.C. / Malta, C.F. / Martins, M.T. / Sousa, P.M. / Matias, P.M. / Schwarz, D. / Ventura, M.R. / Gradler, U. / Bandeiras, T.M.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 1, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1453
Polymers17,7831
Non-polymers3612
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint4 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.059, 56.059, 85.851
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17783.322 Da / Num. of mol.: 1 / Mutation: K133I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-V0Z / N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide / ~{N}-(4-aminophenyl)-7-methyl-2-oxidanylidene-1~{H}-pyrazolo[1,5-a]pyrimidine-6-carboxamide / N-(4-aminophenyl)-7-methyl-2-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-6-carboxamide


Mass: 283.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 1.9 Å3/Da / Density % sol: 35.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15 % PEG 3350, 0.1M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.26→39.64 Å / Num. obs: 37702 / % possible obs: 99.96 % / Redundancy: 17.1 % / Biso Wilson estimate: 10.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 28.98
Reflection shellResolution: 1.26→1.305 Å / Num. unique obs: 3705 / CC1/2: 0.864

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R2H

7r2h


Resolution: 1.26→39.64 Å / SU ML: 0.1831 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.5478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1656 1843 4.83 %
Rwork0.1401 36283 -
obs0.1413 37694 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.65 Å2
Refinement stepCycle: LAST / Resolution: 1.26→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 25 322 1587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321293
X-RAY DIFFRACTIONf_angle_d1.15161744
X-RAY DIFFRACTIONf_chiral_restr0.0793187
X-RAY DIFFRACTIONf_plane_restr0.0086226
X-RAY DIFFRACTIONf_dihedral_angle_d14.786462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.57671300.53222718X-RAY DIFFRACTION99.86
1.29-1.330.25311640.24662726X-RAY DIFFRACTION99.83
1.33-1.370.17211430.14322761X-RAY DIFFRACTION99.93
1.37-1.420.16851620.11942704X-RAY DIFFRACTION100
1.42-1.480.16241410.11852764X-RAY DIFFRACTION100
1.48-1.540.15871240.1182760X-RAY DIFFRACTION100
1.54-1.620.15611290.11342776X-RAY DIFFRACTION100
1.62-1.730.17711220.15072796X-RAY DIFFRACTION100
1.73-1.860.16251510.13382771X-RAY DIFFRACTION100
1.86-2.050.12651500.11382787X-RAY DIFFRACTION100
2.05-2.340.1471310.12982840X-RAY DIFFRACTION100
2.34-2.950.16271390.13852865X-RAY DIFFRACTION100
2.95-39.640.16231570.143015X-RAY DIFFRACTION99.87

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