Structure of PDB 3wq6 Chain B Binding Site BS01

Receptor Information
>3wq6 Chain B (length=474) Species: 4442 (Camellia sinensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFNRTSFPDGFVFGAASSAYQFEGAAKEGGKGPNIWDTFTHEFPGKISNG
STGDVADDFYHRYKEDVKVLKFIGLDGFRMSISWARVLPRGKLSGGVNKE
GIAFYNNVINDLLSKGIQPFITIFHWDLPQALEDEYGGFLSPHIVNDFRD
FAELCFKEFGDRVKHWITMNEPWSYSYGGYDAGLLAPGRCSAFMAFCPKG
NSGTEPYIVTHNLLLSHAAAVKLYKEKYQAYQKGQIGITLVTYWMIPYSN
SKADKDAAQRALDFMYGWFIEPLSFGEYPKSMRRLVGKRLPRFTKEQAML
VKGSFDFLGLNYYIANYVLNVPTSNSVNLSYTTDSLSNQTAFRNGVAIGR
PTGVPAFFMYPKGLKDLLVYTKEKYNDPVIYITENGMGDNNNVTTEEGIK
DPQRVYFYNQHLLSLKNAIAAGVKVKGYFTWAFLDNFEWLSGYTQRFGIV
YVDFKDGLKRYPKHSALWFKKFLL
Ligand information
Ligand IDZPA
InChIInChI=1S/C26H37N3O11S/c27-17(7-4-8-41-16-9-18(31)29(25(16)37)10-13-5-2-1-3-6-13)28-24-22(35)21(34)20(33)15(40-24)12-39-26-23(36)19(32)14(30)11-38-26/h1-3,5-6,14-16,19-24,26,30,32-36H,4,7-12H2,(H2,27,28)/t14-,15-,16-,19+,20-,21+,22-,23-,24-,26+/m1/s1
InChIKeyMKGCRBLJKRCKKQ-OGJWHHEUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)CN2C(=O)CC(C2=O)SCCCC(=N)NC3C(C(C(C(O3)COC4C(C(C(CO4)O)O)O)O)O)O
CACTVS 3.385O[CH]1CO[CH](OC[CH]2O[CH](NC(=N)CCCS[CH]3CC(=O)N(Cc4ccccc4)C3=O)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O
ACDLabs 12.01O=C3N(C(=O)CC3SCCCC(=[N@H])NC2OC(COC1OCC(O)C(O)C1O)C(O)C(O)C2O)Cc4ccccc4
CACTVS 3.385O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)CCCS[C@@H]3CC(=O)N(Cc4ccccc4)C3=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.7.6[H]/N=C(/CCCS[C@@H]1CC(=O)N(C1=O)Cc2ccccc2)\N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO[C@H]4[C@@H]([C@H]([C@@H](CO4)O)O)O)O)O)O
FormulaC26 H37 N3 O11 S
Name4-(N-benzylsuccinimide-3-sulfanyl)-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)butylamidine;
4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2 S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]butanimidamide
ChEMBL
DrugBank
ZINCZINC000098209670
PDB chain3wq6 Chain B Residue 601 [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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PDB3wq6 Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
Q53 H157 W158 N202 E203 W205 S206 Y209 L217 V273 Y275 Y345 F389 E416 W463 E470 W471 S473 Q477 F479
Binding residue
(residue number reindexed from 1)
Q21 H125 W126 N170 E171 W173 S174 Y177 L185 V241 Y243 Y313 F357 E384 W431 E438 W439 S441 Q445 F447
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R111 H157 E203 S206 N343 Y345 E416
Catalytic site (residue number reindexed from 1) R79 H125 E171 S174 N311 Y313 E384
Enzyme Commision number 3.2.1.149: beta-primeverosidase.
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
GO:0050535 beta-primeverosidase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:3wq6, PDBe:3wq6, PDBj:3wq6
PDBsum3wq6
PubMed24753293
UniProtQ7X9A9

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