Structure of PDB 1r33 Chain A Binding Site BS02

Receptor Information
>1r33 Chain A (length=1014) 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
VCPMETAAYVSSHS
Ligand information
Ligand IDLKA
InChIInChI=1S/C6H13NO4S/c7-6-5(11)4(10)3(9)2(1-8)12-6/h2-6,8-11H,1,7H2/t2-,3-,4+,5+,6+/m1/s1
InChIKeyFGVRMLQUWLZGLJ-PQMKYFCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](S1)N)O)O)O)O
CACTVS 3.341N[C@H]1S[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(S1)N)O)O)O)O
ACDLabs 10.04OC1C(O)C(SC(N)C1O)CO
CACTVS 3.341N[CH]1S[CH](CO)[CH](O)[CH](O)[CH]1O
FormulaC6 H13 N O4 S
Name5-thio-alpha-D-mannopyranosylamine;
5-THIO-A/B-D-MANNOPYRANOSYLAMINE;
5-thio-alpha-D-mannosylamine;
5-thio-D-mannosylamine;
5-thio-mannosylamine
ChEMBL
DrugBankDB03414
ZINC
PDB chain1r33 Chain A Residue 1162 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1r33 5-Thio-d-glycopyranosylamines and their amidinium salts as potential transition-state mimics of glycosyl hydrolases: synthesis, enzyme inhibitory activities, X-ray crystallography, and molecular modeling
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H90 D92 W95 D204 F206 Y269 D341 H471 D472 Y727 R876
Binding residue
(residue number reindexed from 1)		H60 D62 W65 D174 F176 Y239 D311 H441 D442 Y697 R846
Annotation score1
Binding affinityMOAD: ic50=0.07mM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1r33, PDBe:1r33, PDBj:1r33
PDBsum1r33
PubMed
UniProtQ24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)

[Back to BioLiP]