Structure of PDB 3u6b Chain B Binding Site BS02

Receptor Information
>3u6b Chain B (length=376) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAAKARGITIN
TSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP
QTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFP
GDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLP
IEDVFSITVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDE
GRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGG
RHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIA
MDDGLRFAIREGGRTVGAGVVAKVLG
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 chain3u6b Chain B Residue 401 [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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PDB3u6b Antibacterial optimization of 4-aminothiazolyl analogues of the natural product GE2270 A: identification of the cycloalkylcarboxylic acids.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		D21 G23 K24 T25 T26 N135 K136 D138 M139 S173 L175
Binding residue
(residue number reindexed from 1)		D20 G22 K23 T24 T25 N122 K123 D125 M126 S160 L162
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D21 K24 T25 T61 H84
Catalytic site (residue number reindexed from 1) D20 K23 T24 T48 H71
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0046677 response to antibiotic
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0032045 guanyl-nucleotide exchange factor complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3u6b, PDBe:3u6b, PDBj:3u6b
PDBsum3u6b
PubMed21999529
UniProtP0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)

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