Structure of PDB 5zc9 Chain A Binding Site BS03

Receptor Information
>5zc9 Chain A (length=378) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQS
GTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMG
ASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKM
FVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFM
RDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF
INTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLIT
TDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE
EDKRTLRDIETFYNTSIEEMPLNVADLI
Ligand information
Ligand IDRCG
InChIInChI=1S/C29H31NO7/c1-30(2)27(32)23-24(17-9-7-6-8-10-17)29(18-11-13-19(34-3)14-12-18)28(33,26(23)31)25-21(36-5)15-20(35-4)16-22(25)37-29/h6-16,23-24,26,31,33H,1-5H3/t23-,24-,26-,28+,29+/m1/s1
InChIKeyDAPAQENNNINUPW-IDAMAFBJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN(C)C(=O)C1C(C2(C(C1O)(c3c(cc(cc3OC)OC)O2)O)c4ccc(cc4)OC)c5ccccc5
OpenEye OEToolkits 2.0.6CN(C)C(=O)[C@@H]1[C@H]([C@]2([C@@]([C@@H]1O)(c3c(cc(cc3OC)OC)O2)O)c4ccc(cc4)OC)c5ccccc5
CACTVS 3.385COc1ccc(cc1)[C]23Oc4cc(OC)cc(OC)c4[C]2(O)[CH](O)[CH]([CH]3c5ccccc5)C(=O)N(C)C
CACTVS 3.385COc1ccc(cc1)[C@@]23Oc4cc(OC)cc(OC)c4[C@]2(O)[C@H](O)[C@@H]([C@H]3c5ccccc5)C(=O)N(C)C
FormulaC29 H31 N O7
Name(1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide;
Rocaglamide;
Rocaglamide A
ChEMBLCHEMBL438139
DrugBankDB15495
ZINCZINC000005664046
PDB chain5zc9 Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5zc9 The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F163 Q195
Binding residue
(residue number reindexed from 1)		F135 Q167
Annotation score1
Binding affinityBindingDB: IC50=47nM,Kd=156nM
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0000339 RNA cap binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0003725 double-stranded RNA binding
GO:0003729 mRNA binding
GO:0003743 translation initiation factor activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008135 translation factor activity, RNA binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0002183 cytoplasmic translational initiation
GO:0006412 translation
GO:0006413 translational initiation
GO:0045944 positive regulation of transcription by RNA polymerase II
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016281 eukaryotic translation initiation factor 4F complex
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0097165 nuclear stress granule

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5zc9, PDBe:5zc9, PDBj:5zc9
PDBsum5zc9
PubMed30595437
UniProtP60842|IF4A1_HUMAN Eukaryotic initiation factor 4A-I (Gene Name=EIF4A1)

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