Structure of PDB 2zx5 Chain A Binding Site BS01

Receptor Information
>2zx5 Chain A (length=441) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMD
AWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWD
PQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGD
LAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAY
KQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWG
VPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQ
LVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIY
GTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAG
TVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAV
Ligand information
Ligand IDZX5
InChIInChI=1S/C18H25N3O4/c1-10-16(23)18(25)17(24)14(21-10)9-20-15(22)7-6-11-8-19-13-5-3-2-4-12(11)13/h2-5,8,10,14,16-19,21,23-25H,6-7,9H2,1H3,(H,20,22)/t10-,14+,16+,17+,18+/m0/s1
InChIKeyQUTVJEWHGONWDR-YCIWZXPNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(N1)CNC(=O)CCc2c[nH]c3c2cccc3)O)O)O
ACDLabs 10.04O=C(NCC1NC(C(O)C(O)C1O)C)CCc3c2ccccc2nc3
OpenEye OEToolkits 1.5.0C[C@H]1[C@H]([C@H]([C@@H]([C@H](N1)CNC(=O)CCc2c[nH]c3c2cccc3)O)O)O
CACTVS 3.341C[CH]1N[CH](CNC(=O)CCc2c[nH]c3ccccc23)[CH](O)[CH](O)[CH]1O
CACTVS 3.341C[C@@H]1N[C@H](CNC(=O)CCc2c[nH]c3ccccc23)[C@@H](O)[C@H](O)[C@@H]1O
FormulaC18 H25 N3 O4
Name3-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}propanamide
ChEMBLCHEMBL1236988
DrugBank
ZINCZINC000038230544
PDB chain2zx5 Chain A Residue 901 [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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PDB2zx5 Structural basis of alpha-fucosidase inhibition by iminocyclitols with K(i) values in the micro- to picomolar range.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		H34 F59 E66 W67 H128 H129 Y171 D224 M225 R254 E266 F290
Binding residue
(residue number reindexed from 1)		H28 F53 E60 W61 H122 H123 Y165 D218 M219 R248 E260 F284
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=12.33,Kd=0.469pM
Enzymatic activity
Enzyme Commision number 3.2.1.51: alpha-L-fucosidase.
Gene Ontology
Molecular Function
GO:0004560 alpha-L-fucosidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006004 fucose metabolic process
GO:0016139 glycoside catabolic process
Cellular Component
GO:0005764 lysosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2zx5, PDBe:2zx5, PDBj:2zx5
PDBsum2zx5
PubMed19967696
UniProtQ9WYE2

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