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- PDB-5a5j: Cytochrome 2C9 P450 inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5a5j
TitleCytochrome 2C9 P450 inhibitor complex
ComponentsCYTOCHROME P450 2C9
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


arachidonic acid 14,15-epoxygenase activity / arachidonic acid 11,12-epoxygenase activity / amide metabolic process / (S)-limonene 6-monooxygenase / (S)-limonene 7-monooxygenase / (R)-limonene 6-monooxygenase / (S)-limonene 6-monooxygenase activity / (S)-limonene 7-monooxygenase activity / (R)-limonene 6-monooxygenase activity / monocarboxylic acid metabolic process ...arachidonic acid 14,15-epoxygenase activity / arachidonic acid 11,12-epoxygenase activity / amide metabolic process / (S)-limonene 6-monooxygenase / (S)-limonene 7-monooxygenase / (R)-limonene 6-monooxygenase / (S)-limonene 6-monooxygenase activity / (S)-limonene 7-monooxygenase activity / (R)-limonene 6-monooxygenase activity / monocarboxylic acid metabolic process / urea metabolic process / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / CYP2E1 reactions / arachidonic acid epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / caffeine oxidase activity / Biosynthesis of maresin-like SPMs / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / monoterpenoid metabolic process / oxidative demethylation / Xenobiotics / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / long-chain fatty acid biosynthetic process / estrogen metabolic process / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / steroid hydroxylase activity / xenobiotic catabolic process / monooxygenase activity / cholesterol metabolic process / xenobiotic metabolic process / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6YF / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2C9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSkerratt, S.E. / de Groot, M.J. / Phillips, C.
CitationJournal: To be Published
Title: Discovery of a Novel Binding Pocket for Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar.
Authors: Skerratt, S.E. / De Groot, M.J. / Phillips, C.
History
DepositionJun 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3763
Polymers54,3231
Non-polymers1,0532
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.290, 91.290, 169.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CYTOCHROME P450 2C9 / (R)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 7-MONOOXYGENASE / ...(R)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 7-MONOOXYGENASE / CYPIIC9 / CYTOCHROME P-450MP / CYTOCHROME P450 MP-4 / CYTOCHROME P450 MP-8 / CYTOCHROME P450 PB-1 / S-MEPHENYTOIN 4-HYDROXYLASE / CYTOCHROME 2C9


Mass: 54322.887 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11712, EC: 1.14.99.38
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-6YF / N-[4-(3-chloranyl-4-cyano-phenoxy)-3,5-dimethoxy-phenyl]-1,1,1-tris(fluoranyl)methanesulfonamide


Mass: 436.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12ClF3N2O5S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→29 Å / Num. obs: 11653 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 3.12 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7

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Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→71.74 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.879 / SU B: 23.539 / SU ML: 0.43 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28792 555 4.8 %RANDOM
Rwork0.21303 ---
obs0.21655 11096 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→71.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 71 0 3717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193785
X-RAY DIFFRACTIONr_bond_other_d0.0020.023656
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9915129
X-RAY DIFFRACTIONr_angle_other_deg0.98638444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28624.036166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69215672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3531520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214193
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02863
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5655.7841817
X-RAY DIFFRACTIONr_mcbond_other3.5455.7811816
X-RAY DIFFRACTIONr_mcangle_it6.018.6562266
X-RAY DIFFRACTIONr_mcangle_other6.0138.6612267
X-RAY DIFFRACTIONr_scbond_it2.8656.0631968
X-RAY DIFFRACTIONr_scbond_other2.8666.0661966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8498.9632863
X-RAY DIFFRACTIONr_long_range_B_refined8.27944.9924241
X-RAY DIFFRACTIONr_long_range_B_other8.27844.994242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 44 -
Rwork0.416 827 -
obs--100 %

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