Structure of PDB 3gph Chain A Binding Site BS01

Receptor Information
>3gph Chain A (length=461) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLPPGPFPLPIIGNLFQLELKNIPKSFTRLAQRFGPVFTLYVGSQRMVVM
HGYKAVKEALLDYKDEFSGRGDLPAFHAHRDRGIIFNNGPTWKDIRRFSL
TTLRNYGKQGNESRIQREAHFLLEALRKTQGQPFDPTFLIGCAPCNVIAD
ILFRKHFDYNDEKFLRLMYLFNENFHLLSTPWLQLYNNFPSFLHYLPGSH
RKVIKNVAEVKEYVSERVKEHHQSLDPNCPRDLTDCLLVEMEKEKHSAER
LYTMDGITVTVADLFFAGTETTSTTLRYGLLILMKYPEIEEKLHEEIDRV
IGPSRIPAIKDRQEMPYMDAVVHEIQRFITLVPSNLPHEATRDTIFRGYL
IPKGTVVVPTLDSVLYDNQEFPDPEKFKPEHFLNENGKFKYSDYFKPFST
GKRVCAGEGLARMELFLLLCAILQHFNLKPLVDPKDIDLSPIHIGFGCIP
PRYKLCVIPRS
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 chain3gph Chain A Residue 500 [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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PDB3gph Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		R100 I114 I115 W122 R126 A299 T303 V364 N367 L368 H370 F430 S431 R435 C437 A438 G439 A443
Binding residue
(residue number reindexed from 1)		R70 I84 I85 W92 R96 A267 T271 V332 N335 L336 H338 F398 S399 R403 C405 A406 G407 A411
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T303 F430 C437
Catalytic site (residue number reindexed from 1) T271 F398 C405
Enzyme Commision number 1.14.13.n7: 4-nitrophenol 2-hydroxylase.
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: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:0018601 4-nitrophenol 2-monooxygenase activity
GO:0019825 oxygen binding
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0030544 Hsp70 protein binding
GO:0046872 metal ion binding
GO:0051879 Hsp90 protein binding
GO:0070330 aromatase activity
GO:0120319 long-chain fatty acid omega-1 hydroxylase activity
Biological Process
GO:0001676 long-chain fatty acid metabolic process
GO:0002933 lipid hydroxylation
GO:0006631 fatty acid metabolic process
GO:0006805 xenobiotic metabolic process
GO:0008202 steroid metabolic process
GO:0009617 response to bacterium
GO:0016098 monoterpenoid metabolic process
GO:0018885 carbon tetrachloride metabolic process
GO:0018910 benzene metabolic process
GO:0018960 4-nitrophenol metabolic process
GO:0019373 epoxygenase P450 pathway
GO:0042197 halogenated hydrocarbon metabolic process
GO:0042759 long-chain fatty acid biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gph, PDBe:3gph, PDBj:3gph
PDBsum3gph
PubMed20463018
UniProtP05181|CP2E1_HUMAN Cytochrome P450 2E1 (Gene Name=CYP2E1)

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