Structure of PDB 1yxq Chain A Binding Site BS02

Receptor Information
>1yxq Chain A (length=356) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRDSYVGDEAQSKRGIL
TLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKAN
REKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPI
YEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEK
LCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPS
FIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQK
EITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEA
GPSIVH
Ligand information
Ligand IDSWI
InChIInChI=1S/C78H132O20/c1-45-23-29-57(79)37-59-19-17-21-61(95-59)41-71(91-15)52(8)68(82)44-70(84)54(10)78(56(12)76(88)48(4)28-32-64-40-66(90-14)36-50(6)94-64)98-74(86)34-26-46(2)24-30-58(80)38-60-20-18-22-62(96-60)42-72(92-16)51(7)67(81)43-69(83)53(9)77(97-73(85)33-25-45)55(11)75(87)47(3)27-31-63-39-65(89-13)35-49(5)93-63/h17-20,23-26,33-34,47-72,75-84,87-88H,21-22,27-32,35-44H2,1-16H3/b33-25+,34-26+,45-23-,46-24+/t47-,48+,49-,50-,51-,52-,53-,54-,55-,56-,57+,58-,59-,60-,61-,62-,63-,64-,65+,66+,67-,68-,69+,70+,71-,72-,75-,76-,77-,78-/m0/s1
InChIKeyRJVBVECTCMRNFG-ITCKPGCBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CO[CH]1C[CH](C)O[CH](CC[CH](C)[CH](O)[CH](C)[CH]2OC(=O)C=CC(=CC[CH](O)C[CH]3O[CH](CC=C3)C[CH](OC)[CH](C)[CH](O)C[CH](O)[CH](C)[CH](OC(=O)C=CC(=CC[CH](O)C[CH]4O[CH](CC=C4)C[CH](OC)[CH](C)[CH](O)C[CH](O)[CH]2C)C)[CH](C)[CH](O)[CH](C)CC[CH]5C[CH](C[CH](C)O5)OC)C)C1
OpenEye OEToolkits 1.5.0CC1CC(CC(O1)CCC(C)C(C(C)C2C(C(CC(C(C(CC3CC=CC(O3)CC(CC=C(C=CC(=O)OC(C(C(CC(C(C(CC4CC=CC(O4)CC(CC=C(C=CC(=O)O2)C)O)OC)C)O)O)C)C(C)C(C(C)CCC5CC(CC(O5)C)OC)O)C)O)OC)C)O)O)C)O)OC
ACDLabs 10.04O=C4OC(C(C)C(O)C(C)CCC1OC(C)CC(OC)C1)C(C)C(O)CC(O)C(C)C(OC)CC2OC(C=CC2)CC(O)CC=C(C=CC(=O)OC(C(C)C(O)CC(O)C(C)C(OC)CC3OC(C=CC3)CC(O)CC=C(C=C4)C)C(C)C(O)C(CCC5OC(CC(OC)C5)C)C)C
CACTVS 3.341CO[C@@H]1C[C@H](C)O[C@@H](CC[C@H](C)[C@H](O)[C@H](C)[C@H]2OC(=O)\C=C\C(=C/C[C@@H](O)C[C@H]3O[C@@H](CC=C3)C[C@H](OC)[C@@H](C)[C@@H](O)C[C@@H](O)[C@H](C)[C@H](OC(=O)/C=C/C(=C/C[C@H](O)C[C@H]4O[C@@H](CC=C4)C[C@H](OC)[C@@H](C)[C@@H](O)C[C@@H](O)[C@@H]2C)C)[C@@H](C)[C@@H](O)[C@H](C)CC[C@H]5C[C@@H](C[C@H](C)O5)OC)C)C1
OpenEye OEToolkits 1.5.0C[C@H]1C[C@H](C[C@@H](O1)CC[C@H](C)[C@@H]([C@H](C)[C@@H]2[C@H]([C@@H](C[C@@H]([C@@H]([C@H](C[C@@H]3CC=C[C@H](O3)C[C@H](C\C=C(\C=C\C(=O)O[C@@H]([C@H]([C@@H](C[C@@H]([C@@H]([C@H](C[C@@H]4CC=C[C@H](O4)C[C@@H](CC=C(\C=C\C(=O)O2)C)O)OC)C)O)O)C)[C@@H](C)[C@H]([C@H](C)CC[C@H]5C[C@@H](C[C@@H](O5)C)OC)O)/C)O)OC)C)O)O)C)O)OC
FormulaC78 H132 O20
NameSWINHOLIDE A
ChEMBL
DrugBank
ZINC
PDB chain1yxq Chain B Residue 600 [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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PDB1yxq Structural basis of swinholide a binding to actin
Resolution2.01 Å
Binding residue
(original residue number in PDB)		D24 D25 Y143 S145 G146 Y169 S344 I345 M355
Binding residue
(residue number reindexed from 1)		D20 D21 Y128 S130 G131 Y154 S329 I330 M340
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003785 actin monomer binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005523 tropomyosin binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0019904 protein domain specific binding
GO:0031013 troponin I binding
GO:0031432 titin binding
GO:0032036 myosin heavy chain binding
GO:0042802 identical protein binding
GO:0048306 calcium-dependent protein binding
GO:0140660 cytoskeletal motor activator activity
Biological Process
GO:0010628 positive regulation of gene expression
GO:0030041 actin filament polymerization
GO:0030240 skeletal muscle thin filament assembly
GO:0048741 skeletal muscle fiber development
GO:0051017 actin filament bundle assembly
GO:0090131 mesenchyme migration
Cellular Component
GO:0001725 stress fiber
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005865 striated muscle thin filament
GO:0005884 actin filament
GO:0030027 lamellipodium
GO:0030175 filopodium
GO:0031941 filamentous actin
GO:0032432 actin filament bundle
GO:0044297 cell body
GO:0098723 skeletal muscle myofibril

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1yxq, PDBe:1yxq, PDBj:1yxq
PDBsum1yxq
PubMed15797212
UniProtP68135|ACTS_RABIT Actin, alpha skeletal muscle (Gene Name=ACTA1)

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