Structure of PDB 5izm Chain A Binding Site BS02

Receptor Information
>5izm Chain A (length=460) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRRVNVNVGVLGHIDSGKTALARALSTTAITLDLGFSCFSVPLPARLRSS
PLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVI
GQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFRGAPIIP
VAAKPGGAPQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFSIGTVMTG
TILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQF
DPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHET
VMGRLMFFSPAPDNFDQEPILDSFNFSQEYLFQEQYLSPRQQWALVEFEK
PVTCPRLCLVIGSRLDADIHTNTCRLAFHGILLHGLEDRNYADSFLPRLK
VYKLKHKDDYSVQLFVGLKVHLSTGELGIIDSFKIHIPGGLLSLTFKRYV
FDTHKRMVQS
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain5izm Chain A Residue 1002 [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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PDB5izm Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		D17 G19 K20 T21 A22 T48 N146 K147 D149 L150 A185 A186 K187
Binding residue
(residue number reindexed from 1)		D15 G17 K18 T19 A20 T31 N113 K114 D116 L117 A152 A153 K154
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=5.92,Kd=1.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) D17 K20 T21 T48 H96
Catalytic site (residue number reindexed from 1) D15 K18 T19 T31 H63
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0035368 selenocysteine insertion sequence binding
GO:0043021 ribonucleoprotein complex binding
Biological Process
GO:0001514 selenocysteine incorporation
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
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:5izm, PDBe:5izm, PDBj:5izm
PDBsum5izm
PubMed27708257
UniProtP57772|SELB_HUMAN Selenocysteine-specific elongation factor (Gene Name=EEFSEC)

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