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- EMDB-78784: CYP3A4 bound to vardenafil -

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Basic information

Entry
Database: EMDB / ID: EMD-78784
TitleCYP3A4 bound to vardenafil
Map data
Sample
  • Complex: Homotrimeric complex of CYP3A4
    • Protein or peptide: Cytochrome P450 3A4
  • Ligand: 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
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: 3.5 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_78784.png

Downloads & links

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Map

FileDownload / File: emd_78784.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 292.4 Å		0.73 Å/pix.
x 400 pix.
= 292.4 Å		0.73 Å/pix.
x 400 pix.
= 292.4 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: 0.0707
Minimum - Maximum-0.6812492 - 0.9275146
Average (Standard dev.)-0.00020272653 (±0.016746609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_78784_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_78784_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 : Homotrimeric complex of CYP3A4

EntireName: Homotrimeric complex of CYP3A4
Components
  • Complex: Homotrimeric complex of CYP3A4
    • Protein or peptide: Cytochrome P450 3A4
  • Ligand: 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Homotrimeric complex of CYP3A4

SupramoleculeName: Homotrimeric complex of CYP3A4 / 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: 55.555539 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: YLYGTHSHGL FKKLGIPGPT PLPFLGNILS YHKGFCMFDM ECHKKYGKVW GFYDGQQPVL AITDPDMIKT VLVKECYSVF TNRRPFGPV GFMKSAISIA EDEEWKRLRS LLSPTFTSGK LKEMVPIIAQ YGDVLVRNLR REAETGKPVT LKDVFGAYSM D VITSTSFG ...String:
YLYGTHSHGL FKKLGIPGPT PLPFLGNILS YHKGFCMFDM ECHKKYGKVW GFYDGQQPVL AITDPDMIKT VLVKECYSVF TNRRPFGPV GFMKSAISIA EDEEWKRLRS LLSPTFTSGK LKEMVPIIAQ YGDVLVRNLR REAETGKPVT LKDVFGAYSM D VITSTSFG VNIDSLNNPQ DPFVENTKKL LRFDFLDPFF LSITVFPFLI PILEVLNICV FPREVTNFLR KSVKRMKESR LE DTQKHRV DFLQLMIDSQ NSKETESHKA LSDLELVAQS IIFIFAGYET TSSVLSFIMY ELATHPDVQQ KLQEEIDAVL PNK APPTYD TVLQMEYLDM VVNETLRLFP IAMRLERVCK KDVEINGMFI PKGVVVMIPS YALHRDPKYW TEPEKFLPER FSKK NKDNI DPYIYTPFGS GPRNCIGMRF ALMNMKLALI RVLQNFSFKP CKETQIPLKL SLGGLLQPEK PVVLKVESRD GTVSG AHHH H

UniProtKB: Cytochrome P450 3A4

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Macromolecule #2: 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7...

MacromoleculeName: 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
type: ligand / ID: 2 / Number of copies: 1 / Formula: VDN
Molecular weightTheoretical: 488.603 Da
Chemical component information

ChemComp-VDN:
2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE

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Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE

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

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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
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: OTHER / Details: CYP3A4 APO cryoEM structure in this study
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Masked: 3.21 Unmasked: 3.7 / Number images used: 164445
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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