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- PDB-5a5i: Cytochrome 2C9 P450 inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5a5i
TitleCytochrome 2C9 P450 inhibitor complex
ComponentsCYTOCHROME P450 2C9
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


arachidonate 14,15-epoxygenase activity / arachidonate 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 ...arachidonate 14,15-epoxygenase activity / arachidonate 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 / arachidonate epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / caffeine oxidase activity / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / oxidative demethylation / Xenobiotics / steroid hydroxylase activity / 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 / xenobiotic catabolic process / xenobiotic metabolic process / cholesterol metabolic process / monooxygenase activity / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-XI1 / Cytochrome P450 2C9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsSkerratt, S.E. / de Groot, M.J. / Phillips, C.
CitationJournal: Med.Chem.Comm. / Year: 2016
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 24, 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 / citation_author / database_2 / pdbx_database_status / struct_site
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _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

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Assembly

Deposited unit
A: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3223
Polymers54,3231
Non-polymers9992
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.217, 92.217, 170.414
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 / CYTOCH ROME P450 MP-4 / CYTOCHROME P450 MP-8 / CYTOCHROME P450 PB-1 / S-MEPH ENYTOIN 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
#2: Chemical ChemComp-XI1 / N-[4-(3-chloranyl-4-cyano-phenoxy)cyclohexyl]-1,1,1-tris(fluoranyl)methanesulfonamide


Mass: 382.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClF3N2O3S
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 27322 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→24.63 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.992 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24501 1733 5 %RANDOM
Rwork0.2124 ---
obs0.21409 32791 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 67 7 3702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193810
X-RAY DIFFRACTIONr_bond_other_d0.0010.023670
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9895166
X-RAY DIFFRACTIONr_angle_other_deg0.89538478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29424.036166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61915672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0861520
X-RAY DIFFRACTIONr_chiral_restr0.1110.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214245
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02867
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_it3.9964.0571817
X-RAY DIFFRACTIONr_mcbond_other3.9954.0581818
X-RAY DIFFRACTIONr_mcangle_it6.0496.062267
X-RAY DIFFRACTIONr_mcangle_other6.0516.0612267
X-RAY DIFFRACTIONr_scbond_it4.3614.5971993
X-RAY DIFFRACTIONr_scbond_other4.3574.5941987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6356.6822891
X-RAY DIFFRACTIONr_long_range_B_refined9.69732.5774223
X-RAY DIFFRACTIONr_long_range_B_other9.69732.5844224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 89 -
Rwork0.335 1795 -
obs--69.65 %

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