Structure of PDB 3dl9 Chain B Binding Site BS02

Receptor Information
>3dl9 Chain B (length=467) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FPPGPPGLPFIGNIYSLAASSELPHVYMRKQSQVYGEIFSLDLGGISTVV
LNGYDVVKECLVHQSEIFADRPCLPLFMKMTKMGGLLNSRYGRGWVDHRR
LAVNSFRYFGYGQKSFESKILEETKFFNDAIETYKGRPFDFKQLITNAVS
NITNLIIFGERFTYEDTDFQHMIELFSENVELAASASVFLYNAFPWIGIL
PFGKHQQLFRNAAVVYDFLSRLIEKASVNRKPQLPQHFVDAYLDEMDQGK
NDPSSTFSKENLIFSVGELIIAGTETTTNVLRWAILFMALYPNIQGQVQK
EIDLIMGPNGKPSWDDKCKMPYTEAVLHEVLRFCNIVPLGIFHATSEDAV
VRGYSIPKGTTVITNLYSVHFDEKYWRDPEVFHPERFLDSSGYFAKKEAL
VPFSLGRRHCLGEHLARMEMFLFFTALLQRFHLHFPHELVPDLKPRLGMT
LQPQPYLICAERRHHHH
Ligand information
Ligand IDV2H
InChIInChI=1S/C28H44O2/c1-18(2)19(3)9-10-20(4)25-13-14-26-22(8-7-15-28(25,26)6)11-12-23-16-24(29)17-27(30)21(23)5/h9-12,18-20,24-27,29-30H,5,7-8,13-17H2,1-4,6H3/b10-9+,22-11+,23-12-/t19-,20+,24+,25+,26-,27-,28+/m0/s1
InChIKeyHKXBNHCUPKIYDM-CGMHZMFXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C(C)C=CC(C)C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C)\C=C\[C@@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C/3\C[C@H](C[C@@H](C3=C)O)O)C
ACDLabs 10.04OC3C(=C)/C(=C\C=C1/CCCC2(C)C(C(/C=C/C(C)C(C)C)C)CCC12)CC(O)C3
CACTVS 3.341CC(C)[CH](C)C=C[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C[CH](O)C3=C
CACTVS 3.341CC(C)[C@@H](C)\C=C\[C@@H](C)[C@H]1CC[C@H]2C(\CCC[C@]12C)=C\C=C/3C[C@@H](O)C[C@H](O)C/3=C
FormulaC28 H44 O2
Name(1S,3R,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraene-1,3-diol;
1-alpha-hydroxy-vitamin D2
ChEMBLCHEMBL1200810
DrugBankDB06410
ZINCZINC000004641374
PDB chain3dl9 Chain B Residue 602 [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)		F214 A250 V253 T488
Binding residue
(residue number reindexed from 1)		F176 A212 V215 T450
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T314 F441 C448
Catalytic site (residue number reindexed from 1) T276 F403 C410
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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