Structure of PDB 3d52 Chain A Binding Site BS02

Receptor Information
>3d52 Chain A (length=1016) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHH
KLKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWA
EISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVL
LQLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRT
HYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDP
KVCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELY
RTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTL
QEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMD
RVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAK
THVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDS
RWPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVS
VTDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGL
ATYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLR
VGNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLF
LPNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNL
VDIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYY
PIPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLG
QGVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPL
DKFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVL
HRTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAP
EVCPMETAAYVSSHSS
Ligand information
Ligand IDGHR
InChIInChI=1S/C13H16ClN3O6/c14-6-1-3-7(4-2-6)15-13(22)23-17-12-11(21)10(20)9(19)8(5-18)16-12/h1-4,8-11,18-21H,5H2,(H,15,22)(H,16,17)/t8-,9-,10+,11-/m1/s1
InChIKeyTZXVKBJPSZOBNV-CHWFTXMASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1NC(=O)O/N=C\2/[C@@H]([C@H]([C@@H]([C@H](N2)CO)O)O)O)Cl
CACTVS 3.341OC[CH]1NC(=NOC(=O)Nc2ccc(Cl)cc2)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0c1cc(ccc1NC(=O)ON=C2C(C(C(C(N2)CO)O)O)O)Cl
CACTVS 3.341OC[C@H]1N\C(=N/OC(=O)Nc2ccc(Cl)cc2)[C@H](O)[C@@H](O)[C@@H]1O
FormulaC13 H16 Cl N3 O6
Name[[(3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)piperidin-2-ylidene]amino] N-(4-chlorophenyl)carbamate
ChEMBL
DrugBank
ZINCZINC000058650008
PDB chain3d52 Chain A Residue 1048 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3d52 Structural analysis of Golgi alpha-mannosidase II inhibitors identified from a focused glycosidase inhibitor screen.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		H90 D92 W95 D204 F206 D341 H471 D472 Y727 R876
Binding residue
(residue number reindexed from 1)		H61 D63 W66 D175 F177 D312 H442 D443 Y698 R847
Annotation score1
Binding affinityMOAD: Ki=520uM
PDBbind-CN: -logKd/Ki=3.28,Ki=520uM
Enzymatic activity
Catalytic site (original residue number in PDB) H90 D92 D204 D341 H471
Catalytic site (residue number reindexed from 1) H61 D63 D175 D312 H442
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3d52, PDBe:3d52, PDBj:3d52
PDBsum3d52
PubMed18759458
UniProtQ24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)

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