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BioLiP

Structure of PDB 1j78 Chain B Binding Site BS01

Receptor Information

>1j78 Chain B (length=447) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

RGRDYEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVV
SLTEACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCTLCMAA
LKHQPQEFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLL
VSYTKSYLSMVGSCCTSASPTVCFLKERLQLKHLSLLTTLSNRVCSQYAA
YGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMA
KELPEHTVKLCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLPELPD
VELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVFLSKVLEPTLKSLGEC
CDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEYKKKLAER
LKAKLPDATPTELAKLVNKRSDFASNCCSINSPPLYCDSEIDAELKN

Ligand information

Ligand ID

VDY

InChI

InChI=1S/C27H44O2/c1-19-10-13-23(28)18-22(19)12-11-21-9-7-17-27(5)24(14-15-25(21)27)20(2)8-6-16-26(3,4)29/h11-12,20,23-25,28-29H,1,6-10,13-18H2,2-5H3/b21-11+,22-12-/t20-,23+,24-,25+,27-/m1/s1

InChIKey

JWUBBDSIWDLEOM-DTOXIADCSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](CCC3=C)O)C
CACTVS 3.341	C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)CCC3=C
CACTVS 3.341	C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)CCC3=C
ACDLabs 10.04	OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)/C(=C)CC3
OpenEye OEToolkits 1.5.0	CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(CCC3=C)O)C

Formula

C27 H44 O2

Name

3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL;
25-HYDROXYVITAMIN D3

PDB chain

1j78 Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	1j78 A structural basis for the unique binding features of the human vitamin D-binding protein.
Resolution	2.31 Å
Binding residue (original residue number in PDB)	E8 L31 Y32 K35 S76 M107
Binding residue (residue number reindexed from 1)	E6 L29 Y30 K33 S74 M98
Annotation score	4

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0003779	actin binding
GO:0005499	vitamin D binding
GO:0090482	vitamin transmembrane transporter activity
GO:1902118	calcidiol binding

	Biological Process
GO:0035461	vitamin transmembrane transport
GO:0042359	vitamin D metabolic process
GO:0051180	vitamin transport

	Cellular Component
GO:0005576	extracellular region
GO:0005615	extracellular space
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0043202	lysosomal lumen
GO:0070062	extracellular exosome
GO:0072562	blood microparticle

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:1j78, PDBe:1j78, PDBj:1j78
PDBsum	1j78
PubMed	11799400
UniProt	P02774\|VTDB_HUMAN Vitamin D-binding protein (Gene Name=GC)

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