Structure of PDB 2bm0 Chain A Binding Site BS01

Receptor Information
>2bm0 Chain A (length=666) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIATITAAVTTCF
WKDHRINIIDAPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWR
QAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDT
FSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADF
DENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLL
DAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVG
RLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGD
LGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEK
LSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVD
ANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGF
EFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYH
EVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGD
LNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFF
DHYQEVPKQVQEKLIK
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 chain2bm0 Chain A Residue 1690 [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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PDB2bm0 Structural Insights Into Fusidic Acid Resistance and Sensitivity in EF-G
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D22 G24 K25 T26 T27 N137 K138 D140 S262 L264
Binding residue
(residue number reindexed from 1)		D19 G21 K22 T23 T24 N114 K115 D117 S239 L241
Annotation score4
Binding affinityMOAD: Ki=440uM
Enzymatic activity
Catalytic site (original residue number in PDB) D22
Catalytic site (residue number reindexed from 1) D19
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0019003 GDP binding
GO:0043022 ribosome binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0032790 ribosome disassembly
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:2bm0, PDBe:2bm0, PDBj:2bm0
PDBsum2bm0
PubMed15843024
UniProtP13551|EFG_THETH Elongation factor G (Gene Name=fusA)

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