Structure of PDB 3mdt Chain B Binding Site BS01

Receptor Information
>3mdt Chain B (length=424) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKM
YRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFN
EKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQ
KPLSQAVKLMLEGITASRNTKRKQLREVRESIRFLRQVGRDWVQRRREAL
KRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTV
MELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYP
PAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDR
FGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPG
QRFGLQEQATLKPLDPVLCTLRPR
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 chain3mdt Chain B Residue 505 [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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PDB3mdt Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K104 Y109 V126 W134 R138 F299 A302 G303 T306 T370 P429 F430 S431 R435 C437 I438 G439 A443
Binding residue
(residue number reindexed from 1)		K46 Y51 V68 W76 R80 F234 A237 G238 T241 T305 P364 F365 S366 R370 C372 I373 G374 A378
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T306 F430 C437
Catalytic site (residue number reindexed from 1) T241 F365 C372
Enzyme Commision number 1.14.14.25: cholesterol 24-hydroxylase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0008395 steroid hydroxylase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0033781 cholesterol 24-hydroxylase activity
GO:0046872 metal ion binding
GO:0062184 testosterone 16-beta-hydroxylase activity
Biological Process
GO:0006699 bile acid biosynthetic process
GO:0006707 cholesterol catabolic process
GO:0006805 xenobiotic metabolic process
GO:0007399 nervous system development
GO:0008203 cholesterol metabolic process
GO:0008207 C21-steroid hormone metabolic process
GO:0016125 sterol metabolic process
GO:0042448 progesterone metabolic process
GO:1900271 regulation of long-term synaptic potentiation
GO:1903044 protein localization to membrane raft
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0030425 dendrite
GO:0042995 cell projection
GO:0045202 synapse
GO:0098793 presynapse
GO:0098794 postsynapse

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3mdt, PDBe:3mdt, PDBj:3mdt
PDBsum3mdt
PubMed20667828
UniProtQ9Y6A2|CP46A_HUMAN Cholesterol 24-hydroxylase (Gene Name=CYP46A1)

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