Structure of PDB 3wq5 Chain A Binding Site BS01

Receptor Information
>3wq5 Chain A (length=475) 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
YVDFKDGLKRYPKHSALWFKKFLLK
Ligand information
Ligand IDVPA
InChIInChI=1S/C19H28N2O9/c20-12(6-9-4-2-1-3-5-9)21-18-16(26)15(25)14(24)11(30-18)8-29-19-17(27)13(23)10(22)7-28-19/h1-5,10-11,13-19,22-27H,6-8H2,(H2,20,21)/t10-,11-,13+,14-,15+,16-,17-,18-,19+/m1/s1
InChIKeySKGTWJNDCFMXKU-GZDQRYBESA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1CO[CH](OC[CH]2O[CH](NC(=N)Cc3ccccc3)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O
CACTVS 3.385O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)Cc3ccccc3)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.7.6c1ccc(cc1)CC(=N)NC2C(C(C(C(O2)COC3C(C(C(CO3)O)O)O)O)O)O
OpenEye OEToolkits 1.7.6[H]/N=C(\Cc1ccccc1)/N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O)O
ACDLabs 12.01O(CC2OC(NC(=[N@H])Cc1ccccc1)C(O)C(O)C2O)C3OCC(O)C(O)C3O
FormulaC19 H28 N2 O9
Name2-phenyl-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)ethylamidine;
2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]e thanimidamide
ChEMBL
DrugBank
ZINCZINC000098209533
PDB chain3wq5 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3wq5 Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
Q53 H157 N202 E203 S206 Y345 F389 E416 W463 E470 W471 S473 Q477 F479
Binding residue
(residue number reindexed from 1)
Q21 H125 N170 E171 S174 Y313 F357 E384 W431 E438 W439 S441 Q445 F447
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=3.85,Ki=140uM
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

View graph for
Biological Process
External links
PDB RCSB:3wq5, PDBe:3wq5, PDBj:3wq5
PDBsum3wq5
PubMed24753293
UniProtQ7X9A9

[Back to BioLiP]