Structure of PDB 3pm0 Chain A Binding Site BS02

Receptor Information
>3pm0 Chain A (length=459) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QAAHLSFARLARRYGDVFQIRLGSCPIVVLNGERAIHQALVQQGSAFADR
PSFASFRVVSGGRSMAFGHYSEHWKVQRRAAHSMMRNFFTRQPRSRQVLE
GHVLSEARELVALLVRGSADGAFLDPRPLTVVAVANVMSAVCFGCRYSHD
DPEFRELLSHNEEFGRTVGAGSLVDVMPWLQYFPNPVRTVFREFEQLNRN
FSNFILDKFLRHCESLRPGAAPRDMMDAFILSAEKKAAGDGARLDLENVP
ATITDIFGASQDTLSTALQWLLLLFTRYPDVQTRVQAELDQVVGRDRLPC
MGDQPNLPYVLAFLYEAMRFSSFVPVTIPHATTANTSVLGYHIPKDTVVF
VNQWSVNHDPLKWPNPENFDPARFLDKDGLINKDLTSRVMIFSVGKRRCI
GEELSKMQLFLFISILAHQCDFRANPNEPAKMNFSYGLTIKPKSFKVNVT
LRESMELLD
Ligand information
Ligand IDBHF
InChIInChI=1S/C19H12O2/c20-17-12-18(14-7-2-1-3-8-14)21-19-15-9-5-4-6-13(15)10-11-16(17)19/h1-12H
InChIKeyVFMMPHCGEFXGIP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)C2=CC(=O)c3ccc4ccccc4c3O2
CACTVS 3.341O=C1C=C(Oc2c1ccc3ccccc23)c4ccccc4
ACDLabs 10.04O=C1c4c(OC(=C1)c2ccccc2)c3ccccc3cc4
FormulaC19 H12 O2
Name2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE;
7,8-BENZOFLAVONE;
ALPHA-NAPHTHOFLAVONE
ChEMBLCHEMBL283196
DrugBankDB07453
ZINCZINC000000038933
PDB chain3pm0 Chain A Residue 800 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3pm0 Structural Characterization of the Complex between {alpha}-Naphthoflavone and Human Cytochrome P450 1B1.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		F134 N228 F231 L264 F268 D326 A330 T334 L509
Binding residue
(residue number reindexed from 1)		F67 N161 F164 L197 F201 D255 A259 T263 L438
Annotation score1
Binding affinityBindingDB: IC50=>10000nM,EC50=35000nM,Ki=16nM
Enzymatic activity
Catalytic site (original residue number in PDB) T334 F463 C470
Catalytic site (residue number reindexed from 1) T263 F392 C399
Enzyme Commision number 1.14.14.1: unspecific monooxygenase.
4.2.1.152: hydroperoxy icosatetraenoate dehydratase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0008395 steroid hydroxylase activity
GO:0016491 oxidoreductase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
GO:0016712 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
GO:0016829 lyase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0070330 aromatase activity
GO:0101020 estrogen 16-alpha-hydroxylase activity
GO:0106256 hydroperoxy icosatetraenoate dehydratase activity
Biological Process
GO:0001525 angiogenesis
GO:0002930 trabecular meshwork development
GO:0006304 DNA modification
GO:0006631 fatty acid metabolic process
GO:0006805 xenobiotic metabolic process
GO:0006809 nitric oxide biosynthetic process
GO:0007155 cell adhesion
GO:0007584 response to nutrient
GO:0008202 steroid metabolic process
GO:0008210 estrogen metabolic process
GO:0008285 negative regulation of cell population proliferation
GO:0008584 male gonad development
GO:0008631 intrinsic apoptotic signaling pathway in response to oxidative stress
GO:0009404 toxin metabolic process
GO:0009636 response to toxic substance
GO:0010575 positive regulation of vascular endothelial growth factor production
GO:0014070 response to organic cyclic compound
GO:0014911 positive regulation of smooth muscle cell migration
GO:0016125 sterol metabolic process
GO:0019369 arachidonate metabolic process
GO:0019373 epoxygenase P450 pathway
GO:0030199 collagen fibril organization
GO:0030325 adrenal gland development
GO:0030336 negative regulation of cell migration
GO:0032088 negative regulation of NF-kappaB transcription factor activity
GO:0032354 response to follicle-stimulating hormone
GO:0032355 response to estradiol
GO:0033629 negative regulation of cell adhesion mediated by integrin
GO:0042445 hormone metabolic process
GO:0042537 benzene-containing compound metabolic process
GO:0042572 retinol metabolic process
GO:0042574 retinal metabolic process
GO:0043065 positive regulation of apoptotic process
GO:0043534 blood vessel endothelial cell migration
GO:0043542 endothelial cell migration
GO:0044849 estrous cycle
GO:0045727 positive regulation of translation
GO:0045766 positive regulation of angiogenesis
GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT
GO:0046466 membrane lipid catabolic process
GO:0046685 response to arsenic-containing substance
GO:0048514 blood vessel morphogenesis
GO:0048545 response to steroid hormone
GO:0061298 retina vasculature development in camera-type eye
GO:0061304 retinal blood vessel morphogenesis
GO:0061548 ganglion development
GO:0070301 cellular response to hydrogen peroxide
GO:0071320 cellular response to cAMP
GO:0071356 cellular response to tumor necrosis factor
GO:0071373 cellular response to luteinizing hormone stimulus
GO:0071387 cellular response to cortisol stimulus
GO:0071393 cellular response to progesterone stimulus
GO:0071407 cellular response to organic cyclic compound
GO:0071548 response to dexamethasone
GO:0071603 endothelial cell-cell adhesion
GO:0071680 response to indole-3-methanol
GO:0097237 cellular response to toxic substance
GO:0097267 omega-hydroxylase P450 pathway
GO:1904681 response to 3-methylcholanthrene
GO:2000377 regulation of reactive oxygen species metabolic process
GO:2000379 positive regulation of reactive oxygen species metabolic process
GO:2000573 positive regulation of DNA biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

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Cellular Component
External links
PDB RCSB:3pm0, PDBe:3pm0, PDBj:3pm0
PDBsum3pm0
PubMed21147782
UniProtQ16678|CP1B1_HUMAN Cytochrome P450 1B1 (Gene Name=CYP1B1)

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