Structure of PDB 3zj6 Chain A Binding Site BS01

Receptor Information

>3zj6 Chain A (length=469) Species: 4060 (Rauvolfia serpentina) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMI
RGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGV
NKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDD
FCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGRTGNPGT
EPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSAS
DVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKG
SYDFVGLNYYTASYVTNASNFSYNTDIHVTYETDRNGVPIGPQSGSDWLL
IYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLK
YLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYND
NFARYPKDSAVWLMNSFHK

Ligand information

Ligand ID

VM2

InChI

InChI=1S/C13H25NO4/c15-7-9-10(12(17)13(18)11(9)16)14-6-8-4-2-1-3-5-8/h8-18H,1-7H2/t9-,10+,11+,12-,13-/m0/s1

InChIKey

PETSRUBXPDOLKZ-QWQWKMKNSA-N

SMILES

Software	SMILES
CACTVS 3.385	OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1NCC2CCCCC2
OpenEye OEToolkits 1.9.2	C1CCC(CC1)CNC2C(C(C(C2O)O)O)CO
OpenEye OEToolkits 1.9.2	C1CCC(CC1)CN[C@@H]2[C@@H]([C@H]([C@@H]([C@H]2O)O)O)CO
CACTVS 3.385	OC[CH]1[CH](O)[CH](O)[CH](O)[CH]1NCC2CCCCC2
ACDLabs 12.01	OC2C(NCC1CCCCC1)C(C(O)C2O)CO

Formula

C13 H25 N O4

Name

(1R,2S,3S,4R,5R)-4-(cyclohexylmethylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol

PDB chain

3zj6 Chain A Residue 1516 [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	3zj6 Ligand Structures of Synthetic Deoxa-Pyranosylamines with Raucaffricine and Strictosidine Glucosidases Provide Structural Insights Into Their Binding and Inhibitory Behaviours.
Resolution	2.4 Å
Binding residue (original residue number in PDB)	Q36 H140 E186 T189 H193 Y347 W392 E420 W469 E476 W477
Binding residue (residue number reindexed from 1)	Q24 H128 E174 T177 H181 Y310 W348 E376 W425 E432 W433
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=6.66,Ki=0.22uM

Enzymatic activity

Catalytic site (original residue number in PDB)	R94 H140 E186 T189 N345 Y347 E420
Catalytic site (residue number reindexed from 1)	R82 H128 E174 T177 N308 Y310 E376
Enzyme Commision number	2.4.1.219: vomilenine glucosyltransferase. 3.2.1.125: raucaffricine beta-glucosidase.

Gene Ontology

	Molecular Function
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008422	beta-glucosidase activity
GO:0016740	transferase activity
GO:0016798	hydrolase activity, acting on glycosyl bonds
GO:0050247	raucaffricine beta-glucosidase activity
GO:0050506	vomilenine glucosyltransferase activity

	Biological Process
GO:0005975	carbohydrate metabolic process
GO:0009820	alkaloid metabolic process
GO:0009821	alkaloid biosynthetic process

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Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:3zj6, PDBe:3zj6, PDBj:3zj6
PDBsum	3zj6
PubMed	25140865
UniProt	Q9SPP9\|RG1_RAUSE Raucaffricine-O-beta-D-glucosidase (Gene Name=RG)

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