Structure of PDB 3mdm Chain A Binding Site BS01

Receptor Information
>3mdm Chain A (length=435) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDS
KMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMET
FNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLG
AQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRD
WVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHET
SANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQV
LKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFE
DPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQ
RLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGW
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 chain3mdm Chain A Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3mdm Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		K104 Y109 L125 V126 W134 R138 F299 A302 G303 T306 A367 T370 P429 F430 S431 R435 C437 I438 G439 A443
Binding residue
(residue number reindexed from 1)		K48 Y53 L69 V70 W78 R82 F243 A246 G247 T250 A311 T314 P373 F374 S375 R379 C381 I382 G383 A387
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T306 F430 C437
Catalytic site (residue number reindexed from 1) T250 F374 C381
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3mdm, PDBe:3mdm, PDBj:3mdm
PDBsum3mdm
PubMed20667828
UniProtQ9Y6A2|CP46A_HUMAN Cholesterol 24-hydroxylase (Gene Name=CYP46A1)

[Back to BioLiP]