Structure of PDB 2npf Chain A Binding Site BS02

Receptor Information
>2npf Chain A (length=822) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAGITI
KSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALR
VTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVS
KEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAF
TIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLE
RAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALL
KVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIK
NCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVP
GKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLT
TSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLT
YMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESE
SSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMA
DDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWA
TKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLA
DPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKA
YLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVL
AARKRHGMKEEVPGWQEYYDKL
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 chain2npf Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2npf Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D29 G31 K32 S33 T34 K159 D161 S213 L215
Binding residue
(residue number reindexed from 1)		D27 G29 K30 S31 T32 K139 D141 S193 L195
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019843 rRNA binding
GO:0042802 identical protein binding
GO:0043022 ribosome binding
GO:0051087 protein-folding chaperone binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0045901 positive regulation of translational elongation
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2npf, PDBe:2npf, PDBj:2npf
PDBsum2npf
PubMed17082187
UniProtP32324|EF2_YEAST Elongation factor 2 (Gene Name=EFT1)

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