Structure of PDB 2f18 Chain A Binding Site BS02

Receptor Information
>2f18 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 IDGB1
InChIInChI=1S/C13H20N2O3/c16-8-11(9-4-2-1-3-5-9)14-6-10-13(18)12(17)7-15-10/h1-5,10-18H,6-8H2/t10-,11+,12+,13-/m1/s1
InChIKeyOGMKEJTXCCFISS-MROQNXINSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04OC1C(NCC1O)CNC(c2ccccc2)CO
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(CO)NCC2C(C(CN2)O)O
OpenEye OEToolkits 1.5.0c1ccc(cc1)[C@H](CO)NC[C@@H]2[C@H]([C@H](CN2)O)O
CACTVS 3.341OC[CH](NC[CH]1NC[CH](O)[CH]1O)c2ccccc2
CACTVS 3.341OC[C@H](NC[C@H]1NC[C@H](O)[C@@H]1O)c2ccccc2
FormulaC13 H20 N2 O3
Name(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL
ChEMBLCHEMBL425723
DrugBank
ZINC
PDB chain2f18 Chain A Residue 1804 [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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PDB2f18 Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		H90 D92 W95 D204 Y269 D340 D341 H471 D472 G877
Binding residue
(residue number reindexed from 1)		H60 D62 W65 D174 Y239 D310 D311 H441 D442 G847
Annotation score1
Binding affinityMOAD: ic50=80uM
PDBbind-CN: -logKd/Ki=4.10,IC50=80uM
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:2f18, PDBe:2f18, PDBj:2f18
PDBsum2f18
PubMed17557336
UniProtQ24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)

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