Structure of PDB 8jce Chain J Binding Site BS03

Receptor Information
>8jce Chain J (length=453) Species: 371094 (Chikungunya virus strain S27-African prototype) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPVYVDIDADSAFLKALQRAYPMFEVEPRQVTPNDAANARAFSHLAIKLI
EQEIDPDSTILDIGSAPARRMMSDRKYHCVCPMRSAEDPERLANYARKLA
SAAGKVLDRNISGKIGDLQAVMAVPDTETPTFCLHTDVSCRQRADVAIYQ
DVYAVHAPTSLYHQAIKGVRLAYWVGFDTTPFMYNAMAGAYPSYSTNWAD
EQVLKAKNIGLCSTDLTEGRRGKLSIMRGKKLEPCDRVLFSVGSTLYPES
RKLLKSWHLPSVFHLKGKLSFTCRCDTVVSCEGYVVKRITMSPGLYGKTT
GYAVTHHADGFLMCKTTDTVDGERVSFSVCTYVPATICDQMTGILATEVT
PEDAQKLLVGLNQRTNTMKNYMIPVVAQAFSKWAKECRKDMEDEKLLGVR
ERTWAFKKQKTHTVYKRPDTQSIQKVQAEFDSFVWSSGLSIPLRTRIKWL
LSK
Ligand information
Ligand IDYG4
InChIInChI=1S/C31H46N12O25P4/c1-40-10-43(25-16(40)26(49)39-30(33)38-25)28-20(48)18(46)12(64-28)6-61-70(53,54)67-72(57,58)68-71(55,56)62-7-13-21(22(59-2)29(65-13)42-9-36-15-23(32)34-8-35-24(15)42)66-69(51,52)60-5-11-17(45)19(47)27(63-11)41-4-3-14(44)37-31(41)50/h3-4,8,11-13,17-22,27-29,36,45-48H,5-7,9-10H2,1-2H3,(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H2,32,34,35)(H,37,44,50)(H3,33,38,39,49)/t11-,12-,13-,17-,18-,19-,20-,21-,22-,27+,28-,29-/m1/s1
InChIKeyPOOGENYSODSFCS-SWDLWUBYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5CNc6c5ncnc6N)OC)OP(=O)(O)OC[C@@H]7[C@H]([C@H]([C@H](O7)N8C=CC(=O)NC8=O)O)O)O)O
OpenEye OEToolkits 2.0.7CN1CN(C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5CNc6c5ncnc6N)OC)OP(=O)(O)OCC7C(C(C(O7)N8C=CC(=O)NC8=O)O)O)O)O
CACTVS 3.385CO[CH]1[CH](O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)N5CN(C)C6=C5N=C(N)NC6=O)O[CH]1N7CNc8c(N)ncnc78
CACTVS 3.385CO[C@@H]1[C@H](O[P](O)(=O)OC[C@H]2O[C@@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)N5CN(C)C6=C5N=C(N)NC6=O)O[C@H]1N7CNc8c(N)ncnc78
FormulaC31 H46 N12 O25 P4
Name[(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8jce Chain J Residue 604 [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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PDB8jce Chikungunya virus Non-structural Protein 1 is a versatile RNA capping and decapping enzyme.
Resolution2.41 Å
Binding residue
(original residue number in PDB)
R41 K99 Y154 Y248 E250
Binding residue
(residue number reindexed from 1)
R40 K98 Y153 Y247 E249
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.7.7.-
2.7.7.19: polynucleotide adenylyltransferase.
2.7.7.48: RNA-directed RNA polymerase.
3.1.3.84: ADP-ribose 1''-phosphate phosphatase.
3.4.22.-
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.1.74: mRNA 5'-phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008174 mRNA methyltransferase activity
Biological Process
GO:0006396 RNA processing
GO:0016556 mRNA modification

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Molecular Function

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Biological Process
External links
PDB RCSB:8jce, PDBe:8jce, PDBj:8jce
PDBsum8jce
PubMed37918803
UniProtQ8JUX6|POLN_CHIKS Polyprotein P1234

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