Structure of PDB 1r34 Chain A Binding Site BS02

Receptor Information

>1r34 Chain A (length=1014) Species: 7227 (Drosophila melanogaster)

CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHK
LKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAE
ISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLL
QLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTH
YSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPK
VCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELYR
TNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTLQ
EYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMDR
VLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKT
HVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDSR
WPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVSV
TDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGLA
TYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLRV
GNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFL
PNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLV
DIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYP
IPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQ
GVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPLD
KFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVLH
RTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAPE
VCPMETAAYVSSHS

Ligand information

• Ligand ID: LKS
• InChI: InChI=1S/C14H20N2O4S/c15-10(6-8-4-2-1-3-5-8)16-14-13(20)12(19)11(18)9(7-17)21-14/h1-5,9,11-14,17-20H,6-7H2,(H2,15,16)/t9-,11-,12+,13+,14+/m1/s1
• InChIKey: WKJQYOUTPMBFSL-CYDRSHDDSA-N
• SMILES:
  CACTVS 3.341: OC[C@H]1S[C@H](NC(=N)Cc2ccccc2)[C@@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: [N@H]=C(NC1SC(C(O)C(O)C1O)CO)Cc2ccccc2
  CACTVS 3.341: OC[CH]1S[CH](NC(=N)Cc2ccccc2)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: [H]/N=C(/Cc1ccccc1)\N[C@@H]2[C@H]([C@H]([C@@H]([C@H](S2)CO)O)O)O
  OpenEye OEToolkits 1.5.0: [H]N=C(Cc1ccccc1)NC2C(C(C(C(S2)CO)O)O)O
• Formula: C14 H20 N2 O4 S
• Name: N-[(1Z)-2-phenylethanimidoyl]-5-thio-alpha-D-mannopyranosylamine;
  N-(1-IMINIO-2-PHENYLETHYL)-5-THIOHEXOPYRANOSYLAMINE BROMIDE;
  2-C-PHENYL-N-(5-THIO-A/B-D-MANNOPYRANOSYL)ACETAMIDINIUM;
  N-[(1Z)-2-phenylethanimidoyl]-5-thio-alpha-D-mannosylamine;
  N-[(1Z)-2-phenylethanimidoyl]-5-thio-D-mannosylamine;
  N-[(1Z)-2-phenylethanimidoyl]-5-thio-mannosylamine
• ZINC: ZINC000006578984
• PDB chain: 1r34 Chain A Residue 1102

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1r34 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
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): H90 D92 W95 D204 R228 S268 Y269 D270 D340 D341 H471 D472 Y727 R876
• Binding residue (residue number reindexed from 1): H60 D62 W65 D174 R198 S238 Y239 D240 D310 D311 H441 D442 Y697 R846
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.9mM

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

External links

• PDB: RCSB:1r34, PDBe:1r34, PDBj:1r34
• PDBsum: 1r34
• UniProt: Q24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)