Structure of PDB 8g60 Chain EF Binding Site BS05

Receptor Information
>8g60 Chain EF (length=443) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGS
FKYAWVLDKLKAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMI
TGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVN
KMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLE
PSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDV
YKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEAL
PGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQI
SAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVD
MVPGKPMCVESFSDYPPLGRFAVRDMRQTVAVGVIKAVDKKAA
Ligand information
Ligand IDZIY
InChIInChI=1S/C57H87N7O15/c1-15-33(8)46-44(66)29-45(67)79-49(32(6)7)48(68)34(9)50(69)58-39(26-30(2)3)54(73)64-25-17-19-41(64)56(75)62(13)43(28-37-20-22-38(77-14)23-21-37)57(76)78-36(11)47(52(71)59-46)60-51(70)42(27-31(4)5)61(12)55(74)40-18-16-24-63(40)53(72)35(10)65/h20-23,30-34,36,39-44,46-47,49,66H,15-19,24-29H2,1-14H3,(H,58,69)(H,59,71)(H,60,70)/t33-,34-,36+,39-,40-,41-,42+,43-,44-,46+,47-,49-/m0/s1
InChIKeyUUSZLLQJYRSZIS-LXNNNBEUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[C@H](C)[C@H]1NC(=O)[C@@H](NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H]2CCCN2C(=O)C(C)=O)[C@@H](C)OC(=O)[C@H](Cc3ccc(OC)cc3)N(C)C(=O)[C@@H]4CCCN4C(=O)[C@H](CC(C)C)NC(=O)[C@@H](C)C(=O)[C@@H](OC(=O)C[C@@H]1O)C(C)C
OpenEye OEToolkits 2.0.7CCC(C)C1C(CC(=O)OC(C(=O)C(C(=O)NC(C(=O)N2CCCC2C(=O)N(C(C(=O)OC(C(C(=O)N1)NC(=O)C(CC(C)C)N(C)C(=O)C3CCCN3C(=O)C(=O)C)C)Cc4ccc(cc4)OC)C)CC(C)C)C)C(C)C)O
OpenEye OEToolkits 2.0.7CC[C@H](C)[C@@H]1C(CC(=O)O[C@H](C(=O)[C@@H](C(=O)N[C@H](C(=O)N2CCC[C@H]2C(=O)N([C@H](C(=O)O[C@@H]([C@@H](C(=O)N1)NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H]3CCCN3C(=O)C(=O)C)C)Cc4ccc(cc4)OC)C)CC(C)C)C)C(C)C)O
CACTVS 3.385CC[CH](C)[CH]1NC(=O)[CH](NC(=O)[CH](CC(C)C)N(C)C(=O)[CH]2CCCN2C(=O)C(C)=O)[CH](C)OC(=O)[CH](Cc3ccc(OC)cc3)N(C)C(=O)[CH]4CCCN4C(=O)[CH](CC(C)C)NC(=O)[CH](C)C(=O)[CH](OC(=O)C[CH]1O)C(C)C
ACDLabs 12.01CC(=O)C(=O)N1CCCC1C(=O)N(C)C(CC(C)C)C(=O)NC1C(=O)NC(C(O)CC(=O)OC(C(C)C)C(=O)C(C)C(=O)NC(CC(C)C)C(=O)N2CCCC2C(=O)N(C)C(Cc2ccc(OC)cc2)C(=O)OC1C)C(C)CC
FormulaC57 H87 N7 O15
Nameplitidepsin
ChEMBLCHEMBL451930
DrugBankDB04977
ZINC
PDB chain8g60 Chain EF Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8g60 mRNA decoding in human is kinetically and structurally distinct from bacteria.
Resolution2.54 Å
Binding residue
(original residue number in PDB)		Y141 I181 Q343 I345 L347 I379 R381 R382 S383 F415 R423 G436
Binding residue
(residue number reindexed from 1)		Y138 I178 Q340 I342 L344 I376 R378 R379 S380 F412 R420 G433
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019900 kinase binding
GO:0019901 protein kinase binding
GO:0060090 molecular adaptor activity
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0044829 positive regulation by host of viral genome replication
GO:0071364 cellular response to epidermal growth factor stimulus
GO:1904714 regulation of chaperone-mediated autophagy
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005853 eukaryotic translation elongation factor 1 complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0030864 cortical actin cytoskeleton
GO:0032587 ruffle membrane
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:0098574 cytoplasmic side of lysosomal membrane
GO:1904813 ficolin-1-rich granule lumen

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8g60, PDBe:8g60, PDBj:8g60
PDBsum8g60
PubMed37020024
UniProtP68104|EF1A1_HUMAN Elongation factor 1-alpha 1 (Gene Name=EEF1A1)

[Back to BioLiP]