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- PDB-6iq5: Crystal Structure of CYP1B1 and Inhibitor Having Azide Group -

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Basic information

Entry
Database: PDB / ID: 6iq5
TitleCrystal Structure of CYP1B1 and Inhibitor Having Azide Group
ComponentsCytochrome P450 1B1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Cytochrome P450 / Inhibitor / CYP1B1 / azide / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


trabecular meshwork development / cellular response to cortisol stimulus / response to indole-3-methanol / Defective CYP1B1 causes Glaucoma / endothelial cell-cell adhesion / benzene-containing compound metabolic process / membrane lipid catabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / ganglion development ...trabecular meshwork development / cellular response to cortisol stimulus / response to indole-3-methanol / Defective CYP1B1 causes Glaucoma / endothelial cell-cell adhesion / benzene-containing compound metabolic process / membrane lipid catabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / ganglion development / retinal blood vessel morphogenesis / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / response to follicle-stimulating hormone / omega-hydroxylase P450 pathway / toxin metabolic process / epoxygenase P450 pathway / arachidonic acid metabolic process / blood vessel endothelial cell migration / DNA modification / estrogen 16-alpha-hydroxylase activity / retinal metabolic process / sterol metabolic process / cellular response to progesterone stimulus / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / cellular response to luteinizing hormone stimulus / negative regulation of cell adhesion mediated by integrin / response to arsenic-containing substance / 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 / collagen fibril organization / estrogen metabolic process / blood vessel morphogenesis / regulation of reactive oxygen species metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of DNA biosynthetic process / adrenal gland development / response to dexamethasone / negative regulation of NF-kappaB transcription factor activity / positive regulation of smooth muscle cell migration / steroid metabolic process / estrous cycle / cellular response to organic cyclic compound / positive regulation of vascular endothelial growth factor production / endothelial cell migration / Endogenous sterols / cellular response to cAMP / nitric oxide biosynthetic process / xenobiotic metabolic process / response to nutrient / negative regulation of cell migration / positive regulation of translation / monooxygenase activity / positive regulation of receptor signaling pathway via JAK-STAT / response to toxic substance / cellular response to hydrogen peroxide / male gonad development / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / response to estradiol / cellular response to tumor necrosis factor / angiogenesis / cell adhesion / iron ion binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / mitochondrion
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-AQ0 / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 1B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.7 Å
AuthorsKubo, M. / Yamamoto, K. / Itoh, T.
CitationJournal: Bioorg. Med. Chem. / Year: 2019
Title: Design and synthesis of selective CYP1B1 inhibitor via dearomatization of alpha-naphthoflavone.
Authors: Kubo, M. / Yamamoto, K. / Itoh, T.
History
DepositionNov 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 1B1
B: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0865
Polymers104,5332
Non-polymers1,5523
Water543
1
A: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2023
Polymers52,2671
Non-polymers9362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-22 kcal/mol
Surface area20270 Å2
MethodPISA
2
B: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8832
Polymers52,2671
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-24 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.190, 135.190, 302.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cytochrome P450 1B1 / CYPIB1


Mass: 52266.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP1B1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16678, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-AQ0 / 2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one


Mass: 319.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 6.8 Å3/Da / Density % sol: 81.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: pH7.4, PEG 8000, ethylene glycol, HEPES, CHPAS

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→47.8 Å / Num. obs: 28823 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 11.5
Reflection shellResolution: 3.7→3.92 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementResolution: 3.7→47.8 Å / Cor.coef. Fo:Fc: 0.795 / Cor.coef. Fo:Fc free: 0.738 / SU B: 141.235 / SU ML: 0.908 / Cross valid method: FREE R-VALUE / ESU R Free: 0.785
RfactorNum. reflection% reflection
Rfree0.39631 1967 6.9 %
Rwork0.35601 --
obs-26522 98.79 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 557.16 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å20 Å2
2---2.5 Å20 Å2
3---5 Å2
Refinement stepCycle: LAST / Resolution: 3.7→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7073 0 110 3 7186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0197378
X-RAY DIFFRACTIONr_bond_other_d00.026961
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9710031
X-RAY DIFFRACTIONr_angle_other_deg3.74315889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1925890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09522.55349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.981151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0861572
X-RAY DIFFRACTIONr_chiral_restr0.0980.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218407
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021863
LS refinement shellResolution: 3.7→3.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.587 133 -
Rwork0.541 1753 -
all-1886 -
obs--86.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6152-0.82343.09872.05220.17593.1363-0.3811-0.4878-0.24580.340.34760.3625-0.1317-0.40680.03350.47480.00040.1580.80850.10820.239511.2632-47.5596-15.3138
20.33990.6298-0.20512.3287-1.00270.4989-0.20150.3098-0.16540.09630.0433-0.3183-0.0630.20780.15820.5366-0.16660.09160.8523-0.08260.201634.6185-41.6686-29.0349
32.8628-1.42641.50840.8969-0.55441.00340.12811.1082-0.14130.5186-0.41570.30880.56820.61210.28761.49540.08270.67450.4328-0.02060.312128.8381-57.9331-20.3139
40.24710.18570.16590.3539-0.11640.7602-0.2610.13430.09130.04420.10430.1377-0.17160.05920.15670.729-0.04150.02140.63990.04970.278821.6742-33.3716-24.7246
50.60540.7562-0.18762.1585-0.27630.0652-0.44650.08150.27110.44380.56840.07130.0927-0.0043-0.12191.0750.3055-0.38470.4666-0.22660.273827.2212-2.419828.166
60.9422-1.4129-0.74342.21051.1020.6019-0.2560.002-0.16340.22510.15360.36180.1128-0.0790.10240.98830.1342-0.15390.52750.20480.177318.0888-26.522213.2286
72.23751.4302-3.33630.9335-2.15124.9928-0.11040.0865-0.0471-0.08330.1090.04450.1684-0.18560.00140.6020.0329-0.00880.4064-0.0290.52228.8648-23.341710.5485
81.70622.32867.04775.12499.417829.40690.75990.7560.16241.817-0.9580.93993.26963.32250.19810.7636-0.43650.1242.3543-0.64370.84788.2612-15.94275.524
911.0774-3.46464.237318.64638.85867.52990.35410.2672-0.38010.3703-0.340.31190.3784-0.0682-0.01410.47220.0371-0.14270.4373-0.10170.711418.26559.688520.3369
1027.6187-19.4874-3.667714.32622.96290.75010.1080.04670.58980.2362-0.1041-0.41270.1394-0.1092-0.00390.59610.0464-00.51260.03350.644710.8229.206912.4744
113.6546.1237-0.678711.1811-1.35440.1905-0.064-0.27590.422-0.19480.0440.52290.0953-0.03230.020.58250.09060.07690.5087-0.02770.50422.8784-9.540317.3673
1210.398-1.42371.75281.88310.02620.72390.28440.182-0.37560.1986-0.3144-0.06990.2761-0.18610.030.5298-0.04950.08960.51210.05930.54230.8449-27.422225.9311
131.0124-0.4363-0.09881.52970.9450.7373-0.492-0.09510.12150.1750.41240.03980.1540.10320.07950.8250.1668-0.20890.5023-0.13020.218629.7047-20.215418.9524
141.67780.77990.08694.2412.00941.23020.00770.23910.2807-0.23450.1571-0.0633-0.08160.0008-0.16480.58820.0129-0.03510.49620.02870.34927.4784-19.68441.7449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 155
2X-RAY DIFFRACTION2A156 - 239
3X-RAY DIFFRACTION3A240 - 312
4X-RAY DIFFRACTION4A313 - 530
5X-RAY DIFFRACTION5B68 - 142
6X-RAY DIFFRACTION6B143 - 200
7X-RAY DIFFRACTION7B201 - 220
8X-RAY DIFFRACTION8B221 - 225
9X-RAY DIFFRACTION9B241 - 246
10X-RAY DIFFRACTION10B251 - 257
11X-RAY DIFFRACTION11B258 - 278
12X-RAY DIFFRACTION12B279 - 301
13X-RAY DIFFRACTION13B302 - 497
14X-RAY DIFFRACTION14B498 - 530

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