Structure of PDB 3u6k Chain B Binding Site BS02

Receptor Information
>3u6k Chain B (length=386) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKA
RGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAA
TDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELL
SQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAID
KPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTG
VEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESE
VYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIK
MVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG
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 chain3u6k Chain B Residue 500 [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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PDB3u6k Antibacterial optimization of 4-aminothiazolyl analogues of the natural product GE2270 A: identification of the cycloalkylcarboxylic acids.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		D21 G23 K24 T25 T26 F46 N135 K136 D138 M139 L175
Binding residue
(residue number reindexed from 1)		D14 G16 K17 T18 T19 F39 N128 K129 D131 M132 L168
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D21 K24 T25 T61 H84
Catalytic site (residue number reindexed from 1) D14 K17 T18 T54 H77
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:3u6k, PDBe:3u6k, PDBj:3u6k
PDBsum3u6k
PubMed21999529
UniProtP0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)

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