Structure of PDB 8k2a Chain Se Binding Site BS02

Receptor Information
>8k2a Chain Se (length=350) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRTNENDPAKHGDQHEGQHYNISPQDLETVFPHGLPPRFVMQVKTFSEAC
LMVRKPALELLHYLKNTSFAYPAIRYLLYGEKGTGKTLSLCHVIHFCAKQ
DWLILHIPDAHLWVKNCRDLLQSSYNKQRFDQPLEASTWLKNFKTTNERF
LNQIKVQEKYVWNKRESTEKGSPLGEVVEQGITRVRNATDAVGIVLKELK
RQSSLGMFHLLVAVDGINALWGRTTLKREDKSPIAPEELALVHNLRKMMK
NDWHGGAIVSALSQTGSLFKPRKAYLPQELLGKEGFDALDPFIPILVSNY
NPKEFESCIQYYLENNWLQHEKAPTEEGKKELLFLSNANPSLLERHCAYL
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 chain8k2a Chain Se 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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PDB8k2a Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R86 Q90 L99 M100 G131 T132 G133 K134 T135 L136 Y348 E392
Binding residue
(residue number reindexed from 1)		R38 Q42 L51 M52 G83 T84 G85 K86 T87 L88 Y300 E344
Annotation score4
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0006915 apoptotic process
GO:0032543 mitochondrial translation
GO:0097190 apoptotic signaling pathway
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005763 mitochondrial small ribosomal subunit
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8k2a, PDBe:8k2a, PDBj:8k2a
PDBsum8k2a
PubMed38942792
UniProtP51398|RT29_HUMAN Small ribosomal subunit protein mS29 (Gene Name=DAP3)

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