Structure of PDB 5n6s Chain A Binding Site BS01

Receptor Information
>5n6s Chain A (length=443) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKKFPEGFLWGVATASYQIEGSPLADGAGMSIWHTFSHTPGNVKNGDTGD
VACDHYNRWKEDIEIIEKLGVKAYRFSISWPRILPEGTGRVNQKGLDFYN
RIIDTLLEKGITPFVTIYHWDLPFALQLKGGWANREIADWFAEYSRVLFE
NFGDRVKNWITLNEPWVVAIVGHLYGVHAPGMRDIYVAFRAVHNLLRAHA
RAVKVFRETVKDGKIGIVFNNGYFEPASEKEEDIRAVRFMHQFNNYPLFL
NPIYRGDYPELVLEFAREYLPENYKDDMSEIQEKIDFVGLNYYSGHLVKF
DPDAPAKVSFVERDLPKTAMGWEIVPEGIYWILKKVKEEYNPPEVYITEN
GAAFDDVVSEDGRVHDQNRIDYLKAHIGQAWKAIQEGVPLKGYFVWSLLD
NFEWAEGYSKRFGIVYVDYSTQKRIVKDSGYWYSNVVKNNGLE
Ligand information
Ligand ID8P5
InChIInChI=1S/C13H22N4O5/c14-17-16-4-2-1-3-15-13(22)9-7-6(5-18)10(19)12(21)11(20)8(7)9/h6-12,14,18-21H,1-5H2/p+1/t6-,7+,8-,9-,10+,11-,12-/m0/s1
InChIKeyAGQBRQFVJQUDGP-MQOZHFKUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C(CCN=[N+]=N)CNC(=O)C1C2C1C(C(C(C2CO)O)O)O
CACTVS 3.385OC[CH]1[CH](O)[CH](O)[CH](O)[CH]2[CH]1[CH]2C(=O)NCCCCN=[N+]=N
OpenEye OEToolkits 2.0.6C(CCN=[N+]=N)CNC(=O)[C@H]1[C@H]2[C@@H]1[C@@H]([C@H]([C@@H]([C@H]2CO)O)O)O
CACTVS 3.385OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@H]2[C@@H]1[C@@H]2C(=O)NCCCCN=[N+]=N
FormulaC13 H23 N4 O5
Nameazanylidene-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)-7-bicyclo[4.1.0]heptanyl]carbonylamino]butylimino]azanium
ChEMBL
DrugBank
ZINCZINC000584905487
PDB chain5n6s Chain A Residue 507 [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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PDB5n6s Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
Q20 H121 W122 N165 E166 W168 V169 E351 W398 E405 W406 F414
Binding residue
(residue number reindexed from 1)
Q18 H119 W120 N163 E164 W166 V167 E349 W396 E403 W404 F412
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.09,Ki=8.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) R77 H121 E166 V169 N293 Y295 E351
Catalytic site (residue number reindexed from 1) R75 H119 E164 V167 N291 Y293 E349
Enzyme Commision number 3.2.1.21: beta-glucosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008422 beta-glucosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0030245 cellulose catabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5n6s, PDBe:5n6s, PDBj:5n6s
PDBsum5n6s
PubMed28463498
UniProtQ08638|BGLA_THEMA Beta-glucosidase A (Gene Name=bglA)

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