Structure of PDB 3dl9 Chain A Binding Site BS01

Receptor Information
>3dl9 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]
GFPPGPPGLPFIGNIYSLAASSELPHVYMRKQSQVYGEIFSLDLGGISTV
VLNGYDVVKECLVHQSEIFADRPCLPLFMKMTKMGGLLNSRYGRGWVDHR
RLAVNSFRYFGYGQKSFESKILEETKFFNDAIETYKGRPFDFKQLITNAV
SNITNLIIFGERFTYEDTDFQHMIELFSENVELAASASVFLYNAFPWIGI
LPFGKHQQLFRNAAVVYDFLSRLIEKASVNRKPQLPQHFVDAYLDEMDQG
KNDPSSTFSKENLIFSVGELIIAGTETTTNVLRWAILFMALYPNIQGQVQ
KEIDLIMGPNGKPSWDDKCKMPYTEAVLHEVLRFCNIVPLGIFHATSEDA
VVRGYSIPKGTTVITNLYSVHFDEKYWRDPEVFHPERFLDSSGYFAKKEA
LVPFSLGRRHCLGEHLARMEMFLFFTALLQRFHLHFPHELVPDLKPRLGM
TLQPQPYLICAERRH
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 chain3dl9 Chain A Residue 601 [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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PDB3dl9 Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2.
Resolution2.721 Å
Binding residue
(original residue number in PDB)		R109 W133 R137 F144 A310 G311 T314 V375 H381 P440 F441 S442 R446 C448 A454
Binding residue
(residue number reindexed from 1)		R72 W96 R100 F107 A273 G274 T277 V338 H344 P403 F404 S405 R409 C411 A417
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T314 F441 C448
Catalytic site (residue number reindexed from 1) T277 F404 C411
Enzyme Commision number 1.14.14.24: vitamin D 25-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: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:0030343 vitamin D3 25-hydroxylase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:1902271 D3 vitamins binding
Biological Process
GO:0006082 organic acid metabolic process
GO:0006629 lipid metabolic process
GO:0006766 vitamin metabolic process
GO:0006805 xenobiotic metabolic process
GO:0010038 response to metal ion
GO:0010164 response to cesium ion
GO:0010212 response to ionizing radiation
GO:0036378 calcitriol biosynthetic process from calciol
GO:0042359 vitamin D metabolic process
GO:0042368 vitamin D biosynthetic 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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dl9, PDBe:3dl9, PDBj:3dl9
PDBsum3dl9
PubMed
UniProtQ6VVX0|CP2R1_HUMAN Vitamin D 25-hydroxylase (Gene Name=CYP2R1)

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