Structure of PDB 4f9f Chain D Binding Site BS02

Receptor Information
>4f9f Chain D (length=464) Species: 264445 (Streptomyces hygroscopicus subsp. limoneus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEIFLASKRAAITYDTPRAWLAPGGTGNVVAEQAGVLNISWIASADSEDD
RRASALNPDGVTMELHSGREILVRLIRHDPAVFRNVQNFMTANLMWAANN
YGWDRWTQPSFGSDAREGWADFGRFTRDFADAILKSSAQSADPVYLVHDY
QLVGVPALLREQRPDAPILLFVHIPWPSADYWRILPKEIRTGILHGMLPA
TTIGFFADRWCRNFLESVADLLPDARIDREAMTVEWRGHRTRLRTMPLGY
SPLTLQLPEGIEEWADGHRLVVHSGRTDPIKNAERAVRAFVLAARGGGLE
KTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGSDTVRIDNDNDVN
HTIACFRRADLLIFNSTVDGQNLSTFEAPLVNERDADVILSETCGAAEVL
GEYCRSVNPFDLVEQAEAISAALAAGPRQRAEAAARRRDAARPWTLEAWV
QAQLDGLAADHAAR
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 chain4f9f Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4f9f Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex.
Resolution2.807 Å
Binding residue
(original residue number in PDB)		R290 N323 N361 D362 V363 T366 N386 L387 S388 E391
Binding residue
(residue number reindexed from 1)		R276 N309 N347 D348 V349 T352 N372 L373 S374 E377
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H182 D383
Catalytic site (residue number reindexed from 1) H173 D369
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:4f9f, PDBe:4f9f, PDBj:4f9f
PDBsum4f9f
PubMed23028689
UniProtQ15JG1|VLDE_STRHL Validamine 7-phosphate valienyltransferase (Gene Name=vldE)

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