Structure of PDB 8xsx Chain CB Binding Site BS03

Receptor Information
>8xsx Chain CB (length=846) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAG
ETRFTDTRKDEQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINL
IDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIK
PVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGN
IMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAERAKKVEDMMKKLWG
DRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEET
AKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPV
TAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYA
FGRVFSGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIE
DVPCGNIVGLVGVDQFLVKTGTITTFEHAHNMRVMKFSVSPVVRVAVEAK
NPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLE
EDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDG
LAEDIDKGEVSARQELKQRARYLAEKYEWDVAEARKIWCFGPDGTGPNIL
TDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVHDVTLHAD
AIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGV
LNRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQC
VFDHWQILPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDNFLDKL
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8xsx Chain CB Residue 1001 [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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PDB8xsx Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D29 G31 K32 S33 T34 N158 K159 D161 S216 L218
Binding residue
(residue number reindexed from 1)		D27 G29 K30 S31 T32 N156 K157 D159 S214 L216
Annotation score3
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:0016787 hydrolase activity
GO:0019901 protein kinase binding
GO:0043022 ribosome binding
GO:0045296 cadherin binding
Biological Process
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006412 translation
GO:0006414 translational elongation
GO:0045727 positive regulation of translation
Cellular Component
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016235 aggresome
GO:0034774 secretory granule lumen
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8xsx, PDBe:8xsx, PDBj:8xsx
PDBsum8xsx
PubMed38942792
UniProtP13639|EF2_HUMAN Elongation factor 2 (Gene Name=EEF2)

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