Structure of PDB 5zc9 Chain A Binding Site BS02

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 IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[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
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5zc9 Chain A Residue 500 [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)		F52 Q59 G79 G81 K82 T83 G335 D337 R362 R365 F366
Binding residue
(residue number reindexed from 1)		F24 Q31 G51 G53 K54 T55 G307 D309 R334 R337 F338
Annotation score3
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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