Structure of PDB 6b9p Chain B Binding Site BS09

Receptor Information
>6b9p Chain B (length=929) Species: 3823 (Canavalia ensiformis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYNTGAGTVPEQLNVHLVPHSHDDVGWLKTVDQYYVGSENYIQEACVEN
VLDSVVMSLQRDPNRKFVFGEMAFFHRWWLEQTPETKELVRKLVKAGQLE
FVNGGWCMHDEATTHYIDMIDHTTLGHRFIQEQFNKIPRAGWQIDPFGHS
AVQGYLLGAELGFDSVHFARIDYQDREKRKAEKSLEVVWRGSKTFGSSAQ
IFANAFPGHYGPPNGFNFEVRNNFVPLQDDPRLFDTNVEERVQNFIDAAL
TQAKITRTNHIMWTMGDDFQYQYAESWFKQMDKLIHHVNKDGRVNALYST
PSIYTEAKNAANQTWPLKIDDYFPYADGRNAYWTGFYTSRSALKDYVRML
SGYYLATRQLGFFAGKKSTKYHAFDLADALGIAQHHDAVSGTAKQHTTND
YAKRLAIGASKAEAVVSSSLACLTSKCSAPASAFSQCHLFNISYCPPTES
SIPDDKSLVVVVYNPLGWSRNEIVRIPVNDANLVVKDSSGNKLEVQYVEM
DDVTANLRSFYVKAYEGEVPKDADVYWSLFKASVPPLGWSTYFISEALNI
GPGDLKMSFSSLTGQLKRMYNSKTGVDIPIQQNYLWYESSEGDFSDYQAS
GAYIFRPNSSVTRVTRGPLVDEVHQKFNSWISQVTRLYKDKDHAEIEFTI
GPIPTDDGVGKEVITRMTSTMATNKEFYTDSNGRDFLKRVRDYREDWPLE
VTQPVAGNYYPLNLGIYTKDEKSEFSVLVDRATGGASIKDGEVELMLHRR
TIRDDGRGVGEPLDEQVCMTCEGLTVRGNYYLSIHKPAAGSRWRRTTGQE
IYSPMLLAFTQENMENWKSSHSTKGIFMDPNYSLPPSVALITLEELDDGL
VLLRLAHLYEPSEDAEYSTLTKVELKKLFATQKIEELREVSLSANQEKSE
MKKMKWSVEGDDFVVELGPMEIRTFLLQF
Ligand information
Ligand IDD0J
InChIInChI=1S/C19H36N4O5/c1-28-14-15-11-23(21-20-15)10-8-6-4-2-3-5-7-9-22-12-17(25)19(27)18(26)16(22)13-24/h11,16-19,24-27H,2-10,12-14H2,1H3/t16-,17+,18-,19-/m1/s1
InChIKeyXGVWMUFCIMYWGD-FCGDIQPGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COCc1cn(nn1)CCCCCCCCCN2CC(C(C(C2CO)O)O)O
OpenEye OEToolkits 2.0.6COCc1cn(nn1)CCCCCCCCCN2C[C@@H]([C@H]([C@@H]([C@H]2CO)O)O)O
CACTVS 3.385COCc1cn(CCCCCCCCCN2C[CH](O)[CH](O)[CH](O)[CH]2CO)nn1
CACTVS 3.385COCc1cn(CCCCCCCCCN2C[C@H](O)[C@@H](O)[C@H](O)[C@H]2CO)nn1
ACDLabs 12.01C(N1CC(C(O)C(O)C1CO)O)CCCCCCCCn2cc(COC)nn2
FormulaC19 H36 N4 O5
Name(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{9-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]nonyl}piperidine-3,4,5-triol
ChEMBL
DrugBank
ZINC
PDB chain6b9p Chain B Residue 1001 [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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PDB6b9p Structural Basis of Outstanding Multivalent Effects in Jack Bean alpha-Mannosidase Inhibition.
Resolution1.996 Å
Binding residue
(original residue number in PDB)		H23 D25 W28 D145 D268 H386 D387 Y625 G788 R789 G790
Binding residue
(residue number reindexed from 1)		H23 D25 W28 D145 D268 H386 D387 Y603 G756 R757 G758
Annotation score1
Binding affinityMOAD: Ki=0.001uM
Enzymatic activity
Enzyme Commision number 3.2.1.24: alpha-mannosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004559 alpha-mannosidase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006013 mannose metabolic process
Cellular Component
GO:0000326 protein storage vacuole
GO:0005773 vacuole

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6b9p, PDBe:6b9p, PDBj:6b9p
PDBsum6b9p
PubMed29722924
UniProtC0HJB3|MANA_CANEN Alpha-mannosidase

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