Structure of PDB 5npe Chain A Binding Site BS04

Receptor Information
>5npe Chain A (length=780) Species: 498211 (Cellvibrio japonicus Ueda107) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVFYKEHKLRNDGLVITTNQGNIRLQFKSEAAIEVLYRADSKQLPSFALA
QPESAIKAQLTETENHLQFSGGTLTARIQKRPFAISYYRDSELLLAEESG
FQVKINFRFYLSPGEKILGGGQRILGMDRRGQRFPLYNRAHYGYSDHSGQ
MYFGLPAIMSSKQYILVFDNSASGAMDIGKTESDILQLEAKSGRSAYILV
AGNSYPSLIENFTQVTGRQPLPPRWALGSFASRFGYRSEAETRATVQKYK
TEDFPLDTIVLDLYWFGKDIKGHMGNLDWDKENFPTPLDMMADFKQQGVK
TVLITEPFVLTSSKRWDDAVKAKALAKDPQGQPKAFELYFGNGGIIDVFS
KEGSRWFSSIYKDLSKQGVAGWWGDLGEPEMHPEDTQHAIGDADTVHNAY
GHRWAEMLYQQQLDQFPELRPFIMMRAGFVGSQRYGMIPWTGDVSRTWGG
LASQVELALQMSLLGFGYIHSDLGGFADGETLDKEMYIRWLQYGVFQPVY
RPHGQDHIPSEPVFQDEETKAILRPLVKLRYRMLPYIYTAAYQNTLTGMP
LMRPLFFSDEKNPALIDNKTSYFWGDSLLVTPITQAGVESVSIPAPKGVW
FDFWKDTRYQTDGAPLTLPTDLHTIPVLVKAGAFMPYVPAVSTTEDYRSD
SLEIHYYADASVPLAQGEIFEDDGKDPNSIKRNQFDLLTLQATHTDNQLH
FQLARTGKGYRGMPERRATTLVIHNASDQYQHLDINGKTIAIAQADCAST
PALACYDQERRQLQLVFTWGREALNLRLHK
Ligand information
Ligand ID948
InChIInChI=1S/C7H13NO4/c9-1-2-3-4(8-3)6(11)7(12)5(2)10/h2-12H,1H2/t2-,3+,4+,5+,6-,7-/m0/s1
InChIKeyGPIFFOGPRPKRHS-DRYVTRLFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C(C1C2C(N2)C(C(C1O)O)O)O
CACTVS 3.385OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H]2N[C@H]12
OpenEye OEToolkits 2.0.6C([C@H]1[C@@H]2[C@@H](N2)[C@@H]([C@H]([C@@H]1O)O)O)O
CACTVS 3.385OC[CH]1[CH](O)[CH](O)[CH](O)[CH]2N[CH]12
FormulaC7 H13 N O4
Name(1~{R},2~{S},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol
ChEMBL
DrugBank
ZINC
PDB chain5npe Chain A Residue 910 [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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PDB5npe 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		F271 D299 W410 D412 R463 W477 D480 F513 H540
Binding residue
(residue number reindexed from 1)		F234 D262 W373 D375 R426 W440 D443 F476 H503
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.00,IC50>100uM
Enzymatic activity
Enzyme Commision number 2.4.1.161: oligosaccharide 4-alpha-D-glucosyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016757 glycosyltransferase activity
GO:0030246 carbohydrate binding
GO:0033825 oligosaccharide 4-alpha-D-glucosyltransferase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5npe, PDBe:5npe, PDBj:5npe
PDBsum5npe
PubMed28776021
UniProtB3PEE6|OL4AG_CELJU Oligosaccharide 4-alpha-D-glucosyltransferase (Gene Name=agd31B)

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