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- EMDB-78782: CYP3A4 bound to ketoconazole -

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Basic information

Entry
Database: EMDB / ID: EMD-78782
TitleCYP3A4 bound to ketoconazole
Map data
Sample
  • Complex: Trimeric complex of CYP3A4 inhibited by ketoconazole
    • Protein or peptide: Cytochrome P450 3A4
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE
  • Ligand: 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine
Keywordsinhibited complex / cytochrome p450 / OXIDOREDUCTASE
Function / homology
Function and homology information


quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / estrogen 2-hydroxylase activity / steroid catabolic process / oxidative demethylation / androgen metabolic process / vitamin D metabolic process / Atorvastatin ADME / steroid hydroxylase activity / Xenobiotics / retinoic acid metabolic process / Phase I - Functionalization of compounds / estrogen metabolic process / long-chain fatty acid biosynthetic process / retinol metabolic process / unspecific monooxygenase / Prednisone ADME / steroid metabolic process / Aspirin ADME / cholesterol metabolic process / intracellular membrane-bounded organelle / xenobiotic catabolic process / steroid binding / xenobiotic metabolic process / lipid metabolic process / monooxygenase activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / : / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsOrta AK / Fraser JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government1AY1AX000035-01 United States
CitationJournal: To Be Published
Title: Structural analysis of CYP3A4 inhibition by Cryo-EM
Authors: Orta AK / Fraser JS
History
DepositionAug 24, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78782.png

Downloads & links

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Map

FileDownload / File: emd_78782.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 233.92 Å		0.73 Å/pix.
x 320 pix.
= 233.92 Å		0.73 Å/pix.
x 320 pix.
= 233.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0719
Minimum - Maximum-0.20154433 - 0.46900266
Average (Standard dev.)0.00003435296 (±0.010812401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_78782_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_78782_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric complex of CYP3A4 inhibited by ketoconazole

EntireName: Trimeric complex of CYP3A4 inhibited by ketoconazole
Components
  • Complex: Trimeric complex of CYP3A4 inhibited by ketoconazole
    • Protein or peptide: Cytochrome P450 3A4
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE
  • Ligand: 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine

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Supramolecule #1: Trimeric complex of CYP3A4 inhibited by ketoconazole

SupramoleculeName: Trimeric complex of CYP3A4 inhibited by ketoconazole / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytochrome P450 3A4

MacromoleculeName: Cytochrome P450 3A4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: unspecific monooxygenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.757812 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAYLYGTHSH GLFKKLGIPG PTPLPFLGNI LSYHKGFCMF DMECHKKYGK VWGFYDGQQP VLAITDPDMI KTVLVKECYS VFTNRRPFG PVGFMKSAIS IAEDEEWKRL RSLLSPTFTS GKLKEMVPII AQYGDVLVRN LRREAETGKP VTLKDVFGAY S MDVITSTS ...String:
MAYLYGTHSH GLFKKLGIPG PTPLPFLGNI LSYHKGFCMF DMECHKKYGK VWGFYDGQQP VLAITDPDMI KTVLVKECYS VFTNRRPFG PVGFMKSAIS IAEDEEWKRL RSLLSPTFTS GKLKEMVPII AQYGDVLVRN LRREAETGKP VTLKDVFGAY S MDVITSTS FGVNIDSLNN PQDPFVENTK KLLRFDFLDP FFLSITVFPF LIPILEVLNI CVFPREVTNF LRKSVKRMKE SR LEDTQKH RVDFLQLMID SQNSKETESH KALSDLELVA QSIIFIFAGY ETTSSVLSFI MYELATHPDV QQKLQEEIDA VLP NKAPPT YDTVLQMEYL DMVVNETLRL FPIAMRLERV CKKDVEINGM FIPKGVVVMI PSYALHRDPK YWTEPEKFLP ERFS KKNKD NIDPYIYTPF GSGPRNCIGM RFALMNMKLA LIRVLQNFSF KPCKETQIPL KLSLGGLLQP EKPVVLKVES RDGTV SGAH HHH

UniProtKB: Cytochrome P450 3A4

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 3 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-Y...

MacromoleculeName: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE
type: ligand / ID: 3 / Number of copies: 3 / Formula: KLN
Molecular weightTheoretical: 531.431 Da
Chemical component information

ChemComp-KLN:
1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE

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Macromolecule #4: 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-y...

MacromoleculeName: 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine
type: ligand / ID: 4 / Number of copies: 3 / Formula: KKK
Molecular weightTheoretical: 531.431 Da
Chemical component information

ChemComp-KKK:
1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
5.0 %Glycerol
100.0 mMPhosphate buffer
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 19000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2v0m

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 29000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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