Structure of PDB 3k9y Chain A Binding Site BS02

Receptor Information
>3k9y Chain A (length=461) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVTDLPGPTNWPLLGSLLEIFWKGGLKKQHDTLAEYHKKYGQIFRMKLGS
FDSVHLGSPSLLEALYRTESAHPQRLEIKPWKAYRDHRNEAYGLMILEGQ
EWQRVRSAFQKKLMKPVEIMKLDKKINEVLADFLERMDELCDERGRIPDL
YSELNKWSFESICLVLYEKRFGLLQKETEEEALTFITAIKTMMSTFGKMM
VTPVELHKRLNTKVWQAHTLAWDTIFKSVKPCIDNRLQRYSQQPGADFLC
DIYQQDHLSKKELYAAVTELQLAAVETTANSLMWILYNLSRNPQAQRRLL
QEVQSVLPDNQTPRAEDLRNMPYLKACLKESMRLTPSVPFTTRTLDKPTV
LGEYALPKGTVLTLNTQVLGSSEDNFEDSHKFRPERWLQKEKKINPFAHL
PFGIGKRMCIGRRLAELQLHLALCWIIQKYDIVATDNEPVEMLHLGILVP
SRELPIAFRPR
Ligand information
Ligand IDCM5
InChIInChI=1S/C23H42O11/c24-11-14-16(26)17(27)19(29)23(32-14)34-21-15(12-25)33-22(20(30)18(21)28)31-10-6-2-5-9-13-7-3-1-4-8-13/h13-30H,1-12H2/t14-,15-,16-,17+,18-,19-,20-,21-,22-,23-/m1/s1
InChIKeyRVTGFZGNOSKUDA-ZNGNCRBCSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O(CCCCCC1CCCCC1)C3OC(C(OC2OC(CO)C(O)C(O)C2O)C(O)C3O)CO
OpenEye OEToolkits 1.5.0C1CCC(CC1)CCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](OCCCCCC3CCCCC3)O[CH]2CO)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](OCCCCCC3CCCCC3)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1CCC(CC1)CCCCCOC2C(C(C(C(O2)CO)OC3C(C(C(C(O3)CO)O)O)O)O)O
FormulaC23 H42 O11
Name5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE;
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE;
CYMAL-5
ChEMBL
DrugBankDB04664
ZINCZINC000014881288
PDB chain3k9y Chain A Residue 516 [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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PDB3k9y Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		M246 S247 F249
Binding residue
(residue number reindexed from 1)		M193 S194 F196
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T330 F455 C462
Catalytic site (residue number reindexed from 1) T277 F402 C409
Enzyme Commision number 1.14.15.16: vitamin D3 24-hydroxylase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0008403 25-hydroxycholecalciferol-24-hydroxylase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0030342 1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity
GO:0046872 metal ion binding
GO:0062180 25-hydroxycholecalciferol-23-hydroxylase activity
GO:0062181 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity
GO:0070576 vitamin D 24-hydroxylase activity
GO:0070643 vitamin D 25-hydroxylase activity
Biological Process
GO:0001649 osteoblast differentiation
GO:0006629 lipid metabolic process
GO:0008202 steroid metabolic process
GO:0033280 response to vitamin D
GO:0042359 vitamin D metabolic process
GO:0042369 vitamin D catabolic process
GO:0071305 cellular response to vitamin D
Cellular Component
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3k9y, PDBe:3k9y, PDBj:3k9y
PDBsum3k9y
PubMed19961857
UniProtQ09128|CP24A_RAT 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial (Gene Name=Cyp24a1)

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