Structure of PDB 3ddf Chain A Binding Site BS02

Receptor Information
>3ddf Chain A (length=1015) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHK
LKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAE
ISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLL
QLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTH
YSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPK
VCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELYR
TNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTLQ
EYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMDR
VLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKT
HVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDSR
WPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVSV
TDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGLA
TYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLRV
GNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFL
PNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLV
DIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYP
IPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQ
GVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPLD
KFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVLH
RTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAPE
VCPMETAAYVSSHSS
Ligand information
Ligand IDGB6
InChIInChI=1S/C13H18N2O4/c16-7-10(8-4-2-1-3-5-8)14-6-9-11(17)12(18)13(19)15-9/h1-5,9-12,14,16-18H,6-7H2,(H,15,19)/t9-,10+,11-,12-/m1/s1
InChIKeyKRKSNZJFCXFNFF-WRWGMCAJSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH](NC[CH]1NC(=O)[CH](O)[CH]1O)c2ccccc2
ACDLabs 10.04O=C2NC(CNC(c1ccccc1)CO)C(O)C2O
CACTVS 3.341OC[C@H](NC[C@H]1NC(=O)[C@H](O)[C@@H]1O)c2ccccc2
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(CO)NCC2C(C(C(=O)N2)O)O
OpenEye OEToolkits 1.5.0c1ccc(cc1)[C@H](CO)NC[C@@H]2[C@H]([C@H](C(=O)N2)O)O
FormulaC13 H18 N2 O4
Name(3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidin-2-one
ChEMBLCHEMBL476925
DrugBank
ZINCZINC000024982350
PDB chain3ddf Chain A Residue 4001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ddf Functionalized pyrrolidine inhibitors of human type II alpha-mannosidases as anti-cancer agents: optimizing the fit to the active site
Resolution1.2 Å
Binding residue
(original residue number in PDB)		H90 D92 W95 D204 Y269 D340 D341 H471 D472 Y727 G877
Binding residue
(residue number reindexed from 1)		H60 D62 W65 D174 Y239 D310 D311 H441 D442 Y697 G847
Annotation score1
Binding affinityMOAD: Ki=67uM
PDBbind-CN: -logKd/Ki=4.66,Ki=22uM
Enzymatic activity
Catalytic site (original residue number in PDB) H90 D92 D204 D341 H471
Catalytic site (residue number reindexed from 1) H60 D62 D174 D311 H441
Enzyme Commision number 3.2.1.114: mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004559 alpha-mannosidase activity
GO:0004572 mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity
GO:0015923 mannosidase 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
GO:0006486 protein glycosylation
GO:0006491 N-glycan processing
GO:0016063 rhodopsin biosynthetic process
GO:0035010 encapsulation of foreign target
Cellular Component
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0016020 membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ddf, PDBe:3ddf, PDBj:3ddf
PDBsum3ddf
PubMed18599296
UniProtQ24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)

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