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- PDB-7n6f: Co-complex CYP46A1 with compound 3f -

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Basic information

Entry
Database: PDB / ID: 7n6f
TitleCo-complex CYP46A1 with compound 3f
ComponentsCholesterol 24-hydroxylase
KeywordsOXIDOREDUCTASE / cyp46a1 / ch24h / sbdd / drug discovery
Function / homology
Function and homology information


cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / bile acid biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / steroid hydroxylase activity / cholesterol catabolic process ...cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / bile acid biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / steroid hydroxylase activity / cholesterol catabolic process / regulation of long-term synaptic potentiation / Endogenous sterols / xenobiotic metabolic process / presynapse / nervous system development / postsynapse / iron ion binding / dendrite / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Cholesterol 24-hydroxylase / Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-0I1 / PROTOPORPHYRIN IX CONTAINING FE / Cholesterol 24-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLane, W. / Gay, S.C.
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Design and synthesis of aryl-piperidine derivatives as potent and selective PET tracers for cholesterol 24-hydroxylase (CH24H)
Authors: Ikeda, S. / Kajita, Y. / Miyamoto, M. / Matsumiya, K. / Ishii, T. / Nishi, T. / Gay, S.C. / Lane, W. / Constantinescu, C.C. / Alagille, D. / Papin, C. / Tamagnan, G. / Kuroita, T. / Koike, T.
History
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02611
Polymers54,4351
Non-polymers1,59210
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.943, 63.585, 123.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cholesterol 24-hydroxylase / CH24H / Cholesterol 24-monooxygenase / Cholesterol 24S-hydroxylase / Cytochrome P450 46A1


Mass: 54434.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46A1, CYP46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6A2, cholesterol 24-hydroxylase

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Non-polymers , 5 types, 322 molecules

#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-0I1 / (3-fluoroazetidin-1-yl){1-[4-(4-fluorophenyl)pyrimidin-5-yl]piperidin-4-yl}methanone


Mass: 358.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20F2N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.4M CaCl2, 10-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 81954 / % possible obs: 90.42 % / Redundancy: 6.4 % / Rpim(I) all: 0.02 / Rsym value: 0.048 / Net I/σ(I): 31.95
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5294 / CC1/2: 0.869 / Rpim(I) all: 0.227 / Rsym value: 0.521 / % possible all: 55.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LRL

7lrl


Resolution: 1.4→30.81 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.948 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1847 4097 4.999 %
Rwork0.1597 77857 -
all0.161 --
obs-81954 90.42 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.014 Å2-0 Å2-0 Å2
2--0.004 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 109 312 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173768
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.6855276
X-RAY DIFFRACTIONr_angle_other_deg1.5261.5968680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81720.766222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97415694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2191539
X-RAY DIFFRACTIONr_chiral_restr0.1040.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024370
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02944
X-RAY DIFFRACTIONr_nbd_refined0.2340.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23580
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21839
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1780.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.211
X-RAY DIFFRACTIONr_nbd_other0.210.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.213
X-RAY DIFFRACTIONr_mcbond_it1.751.7331812
X-RAY DIFFRACTIONr_mcbond_other1.7361.7321811
X-RAY DIFFRACTIONr_mcangle_it2.5252.5982276
X-RAY DIFFRACTIONr_mcangle_other2.5272.5982277
X-RAY DIFFRACTIONr_scbond_it2.9472.1012067
X-RAY DIFFRACTIONr_scbond_other2.9472.1022068
X-RAY DIFFRACTIONr_scangle_it4.5232.9932976
X-RAY DIFFRACTIONr_scangle_other4.5222.9952977
X-RAY DIFFRACTIONr_lrange_it5.80320.9414465
X-RAY DIFFRACTIONr_lrange_other5.80320.954466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2471970.243606X-RAY DIFFRACTION57.1193
1.436-1.4760.2592390.2254280X-RAY DIFFRACTION70.2581
1.476-1.5180.232630.2045213X-RAY DIFFRACTION86.9068
1.518-1.5650.22630.1825143X-RAY DIFFRACTION88.856
1.565-1.6160.1912790.1715085X-RAY DIFFRACTION90.4858
1.616-1.6730.22700.1695038X-RAY DIFFRACTION92.4739
1.673-1.7360.1742670.1594911X-RAY DIFFRACTION93.8554
1.736-1.8070.182380.1614855X-RAY DIFFRACTION95.2853
1.807-1.8870.1812480.154712X-RAY DIFFRACTION96.9507
1.887-1.9790.1692460.1484513X-RAY DIFFRACTION97.0234
1.979-2.0860.1781980.1494390X-RAY DIFFRACTION98.118
2.086-2.2130.1841830.1444171X-RAY DIFFRACTION97.9528
2.213-2.3650.172130.1413901X-RAY DIFFRACTION98.5625
2.365-2.5540.1881990.1463658X-RAY DIFFRACTION98.8974
2.554-2.7970.1961800.1613391X-RAY DIFFRACTION99.222
2.797-3.1270.1871850.1633066X-RAY DIFFRACTION99.4798
3.127-3.6080.1641350.1572776X-RAY DIFFRACTION99.3176
3.608-4.4150.1611310.1462329X-RAY DIFFRACTION98.994
4.415-6.2230.1921130.1591828X-RAY DIFFRACTION98.7284
6.223-30.80.234500.209991X-RAY DIFFRACTION89.3562

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