Structure of PDB 3ibd Chain A Binding Site BS01

Receptor Information

>3ibd Chain A (length=465) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVM
LCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRF
SVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITAN
IICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHF
PGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKS
NAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYRE
IEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSF
RGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFI
PFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGV
GKIPPTYQIRFLPRH

Ligand information

Ligand ID

HEM

InChI

InChI=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-;

InChIKey

KABFMIBPWCXCRK-RGGAHWMASA-L

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	Cc1c2n3c(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 3.385	CC1=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 12.01	C=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

Formula

C34 H32 Fe N4 O4

Name

PROTOPORPHYRIN IX CONTAINING FE;
HEME

PDB chain

3ibd Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3ibd Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	R98 V113 I114 W121 R125 A298 G299 T302 T303 L363 V367 H369 P428 F429 S430 R434 C436 L437 G438 A442
Binding residue (residue number reindexed from 1)	R71 V86 I87 W94 R98 A271 G272 T275 T276 L336 V340 H342 P401 F402 S403 R407 C409 L410 G411 A415
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	T302 F429 C436
Catalytic site (residue number reindexed from 1)	T275 F402 C409
Enzyme Commision number	1.14.13.-

Gene Ontology

	Molecular Function
GO:0004497	monooxygenase activity
GO:0005506	iron ion binding
GO:0008390	testosterone 16-alpha-hydroxylase activity
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:0062184	testosterone 16-beta-hydroxylase activity
GO:0062187	anandamide 8,9 epoxidase activity
GO:0062188	anandamide 11,12 epoxidase activity
GO:0062189	anandamide 14,15 epoxidase activity
GO:0101021	estrogen 2-hydroxylase activity

	Biological Process
GO:0006629	lipid metabolic process
GO:0006805	xenobiotic metabolic process
GO:0008202	steroid metabolic process
GO:0019373	epoxygenase P450 pathway
GO:0042178	xenobiotic catabolic process
GO:0042180	cellular ketone metabolic process

	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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Cellular Component

External links

PDB	RCSB:3ibd, PDBe:3ibd, PDBj:3ibd
PDBsum	3ibd
PubMed	20061448
UniProt	P20813\|CP2B6_HUMAN Cytochrome P450 2B6 (Gene Name=CYP2B6)

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