Structure of PDB 5em4 Chain A Binding Site BS01

Receptor Information
>5em4 Chain A (length=460) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVL
CGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFS
LATMRDFGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIIC
SIVFGKRFDYKDPVFLRLLDLFFQSFSLISSFSSQVFELFSGFLKYFPGT
HRQIYRNLQEINTWIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPS
SEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQ
VIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGY
VIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFS
LGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPSGVGNVPP
SYQIRFLARH
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain5em4 Chain A Residue 501 [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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PDB5em4 Coumarin Derivatives as Substrate Probes of Mammalian Cytochromes P450 2B4 and 2B6: Assessing the Importance of 7-Alkoxy Chain Length, Halogen Substitution, and Non-Active Site Mutations.
Resolution3.02 Å
Binding residue
(original residue number in PDB)		R98 R125 G299 T303 I363 H369 F429 S430 R434 C436 L437 G438 A442
Binding residue
(residue number reindexed from 1)		R70 R97 G269 T273 I333 H339 F399 S400 R404 C406 L407 G408 A412
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T302 F429 C436
Catalytic site (residue number reindexed from 1) T272 F399 C406
Enzyme Commision number 1.14.14.1: unspecific monooxygenase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0008392 arachidonate epoxygenase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular 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:0020037 heme binding
GO:0046872 metal ion binding
GO:0070330 aromatase activity
Biological Process
GO:0006805 xenobiotic metabolic process
GO:0019373 epoxygenase P450 pathway
Cellular Component
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5em4, PDBe:5em4, PDBj:5em4
PDBsum5em4
PubMed26982502
UniProtP00178|CP2B4_RABIT Cytochrome P450 2B4 (Gene Name=CYP2B4)

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