Structure of PDB 8iyf Chain A Binding Site BS01

Receptor Information
>8iyf Chain A (length=475) Species: 264445 (Streptomyces hygroscopicus subsp. limoneus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSEIFLASKRAAITYDTDPATGEPRAWLAPGGTGNVVAEQAGVLNISWIA
SADSEDDRRASALNPDGVTMELHSGREILVRLIRHDPAVFRNVQNFMTAN
LMWAANNYGWDRWTQPSFGSDAREGWADFGRFTRDFADAILKSSAQSADP
VYLVHDYQLVGVPALLREQRPDAPILLFVAIPWPSADYWRILPKEIRTGI
LHGMLPATTIGFFADRWCRNFLESVADLLPDARIDREAMTVEWRGHRTRL
RTMPLGYSPLTLPQLPEGIEEWADGHRLVVHSGRTDPIKNAERAVRAFVL
AARGGGLEKTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGSDTVR
IDNDNDVNHTIACFRRADLLIFNSTVDGQNLSTFEAPLVNERDADVILSE
TCGAAEVLGEYCRSVNPFDLVEQAEAISAALAAGPRQRAEAAARRRDAAR
PWTLEAWVQAQLDGLAADHAARTAT
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8iyf 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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PDB8iyf Structure of VldE-H182A in complex with GDP
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R290 K295 N323 N361 D362 V363 T366 N386 L387 S388 E391
Binding residue
(residue number reindexed from 1)		R284 K289 N317 N355 D356 V357 T360 N380 L381 S382 E385
Annotation score4
Enzymatic activity
Enzyme Commision number 2.5.1.135: validamine 7-phosphate valienyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016740 transferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0005992 trehalose biosynthetic process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8iyf, PDBe:8iyf, PDBj:8iyf
PDBsum8iyf
PubMed
UniProtQ15JG1|VLDE_STRHL Validamine 7-phosphate valienyltransferase (Gene Name=vldE)

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