Structure of PDB 4re4 Chain A Binding Site BS01

Receptor Information
>4re4 Chain A (length=483) Species: 39946 (Oryza sativa Indica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAPFTYWLNPEIYDAGGLSRRAFPEGFVFGTAASAYQVEGMAKQGGRGPS
IWDAFIEKPGTIPNNATADVTVDEYHRYKEDVNIMKNMGFDAYRFSISWS
RIFPNGTGMVNQEGVDYYNRLIDYMVKKGIKPYANLYHYDLPLALHEQYL
GWLSPNIVEAFADYADFCFQTFGDRVKDWFTFNEPRCVAALGYDNGFHAP
GRCSGCDAGGNSTTEPYLAAHHLILSHAAAVKRYREKYQLYQKGRIGILL
DFVWYEPFSDSNADRAAAQRARDFHLGWFLDPIIHGRYPYSMLEIVKDRM
PTFSDEESRMVKDSIDYVGINHYTSFYMKDPGPWNLTPTSYQDDWHVGFA
YERNGVPIGAQANSYWLYIVPWGINKAVTYVKETYGNPTMILSENGMDQP
GNVSITQGVHDTVRIRYYRNYITELKKAIDDGAKVIGYFAWSLLDNFEWR
LGYTSRFGIVYVDYKTLKRYPKDSAFWFKNMLS
Ligand information
Ligand IDIFM
InChIInChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
InChIKeyQPYJXFZUIJOGNX-HSUXUTPPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1CNC[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
ACDLabs 10.04OC1C(CO)CNCC1O
CACTVS 3.341OC[C@H]1CNC[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1C(C(C(CN1)O)O)CO
FormulaC6 H13 N O3
Name5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE;
Afegostat;
isofagomine;
(3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
ChEMBLCHEMBL206468
DrugBankDB04545
ZINCZINC000003813668
PDB chain4re4 Chain A Residue 501 [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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PDB4re4 A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides
Resolution2.29 Å
Binding residue
(original residue number in PDB)		Q32 H133 E179 Y318 E389 W436 E443 W444 F452
Binding residue
(residue number reindexed from 1)		Q37 H138 E184 Y323 E394 W441 E448 W449 F457
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.87,Ki=135nM
Enzymatic activity
Catalytic site (original residue number in PDB) R89 H133 E179 C182 N316 Y318 E389
Catalytic site (residue number reindexed from 1) R94 H138 E184 C187 N321 Y323 E394
Enzyme Commision number 3.2.1.25: beta-mannosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004565 beta-galactosidase activity
GO:0008422 beta-glucosidase activity
GO:0033907 beta-D-fucosidase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4re4, PDBe:4re4, PDBj:4re4
PDBsum4re4
PubMed
UniProtA2YPH1

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