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- PDB-7pmt: Human Cyclophilin D in complex with N-[(5-ethyl-4-oxo-1,2,3,4,5,6... -

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Basic information

Entry
Database: PDB / ID: 7pmt
TitleHuman Cyclophilin D in complex with N-[(5-ethyl-4-oxo-1,2,3,4,5,6- hexahydro-1,5-benzodiazocin-8-yl)methyl]-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-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
Similarity search - Domain/homology
Chem-7UO / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 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
DepositionSep 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,2713
Polymers17,7831
Non-polymers4882
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.153, 57.153, 87.703
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-610-

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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-7UO / ~{N}-[(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)methyl]-7-methyl-2-oxidanylidene-1,3-dihydropyrazolo[1,5-a]pyrimidine-6-carboxamide


Mass: 409.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
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: 0.97926 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: 0.97926 Å / Relative weight: 1
ReflectionResolution: 0.98→47.88 Å / Num. obs: 79560 / % possible obs: 95.63 % / Redundancy: 16.1 % / Biso Wilson estimate: 7.83 Å2 / CC1/2: 1 / Net I/σ(I): 28.61
Reflection shellResolution: 0.983→1.018 Å / Num. unique obs: 5672 / CC1/2: 0.771

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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: 7NHB

7nhb
PDB Unreleased entry


Resolution: 0.98→47.88 Å / SU ML: 0.1121 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.2714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1476 3897 4.9 %
Rwork0.1307 75659 -
obs0.1315 79556 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.21 Å2
Refinement stepCycle: LAST / Resolution: 0.98→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 34 311 1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541303
X-RAY DIFFRACTIONf_angle_d0.98031758
X-RAY DIFFRACTIONf_chiral_restr0.0856186
X-RAY DIFFRACTIONf_plane_restr0.0068234
X-RAY DIFFRACTIONf_dihedral_angle_d14.3274462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.5107930.52811737X-RAY DIFFRACTION62.5
0.99-1.010.373990.43061966X-RAY DIFFRACTION70.45
1.01-1.020.35151130.33142126X-RAY DIFFRACTION76.39
1.02-1.030.29341160.26592279X-RAY DIFFRACTION82.33
1.03-1.050.22271210.21372483X-RAY DIFFRACTION89.24
1.05-1.060.16671400.16092672X-RAY DIFFRACTION95.48
1.06-1.080.1411470.12882758X-RAY DIFFRACTION99.45
1.08-1.10.11611420.11072814X-RAY DIFFRACTION100
1.1-1.120.11571520.09272770X-RAY DIFFRACTION100
1.12-1.140.11141420.09162805X-RAY DIFFRACTION100
1.14-1.160.11551340.09542805X-RAY DIFFRACTION100
1.16-1.180.11851360.10132798X-RAY DIFFRACTION100
1.18-1.210.13441360.1092795X-RAY DIFFRACTION100
1.21-1.240.1391470.1182807X-RAY DIFFRACTION100
1.24-1.270.12851600.12612801X-RAY DIFFRACTION100
1.27-1.30.15151450.13142810X-RAY DIFFRACTION100
1.3-1.340.13091410.11142807X-RAY DIFFRACTION100
1.34-1.380.13451540.10632807X-RAY DIFFRACTION100
1.38-1.430.11661430.11062826X-RAY DIFFRACTION100
1.43-1.490.12741560.10832806X-RAY DIFFRACTION100
1.49-1.560.14561440.10892830X-RAY DIFFRACTION100
1.56-1.640.12941470.11872838X-RAY DIFFRACTION100
1.64-1.740.12641350.12642856X-RAY DIFFRACTION100
1.74-1.880.1441780.1262829X-RAY DIFFRACTION100
1.88-2.070.13991410.12212879X-RAY DIFFRACTION100
2.07-2.370.12081380.12452910X-RAY DIFFRACTION100
2.37-2.980.16711560.13942930X-RAY DIFFRACTION100
2.98-47.880.16781410.13943115X-RAY DIFFRACTION99.94

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