Structure of PDB 7lw3 Chain A Binding Site BS02

Receptor Information
>7lw3 Chain A (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQL
CQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFF
TYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKF
PLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
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 chain7lw3 Chain A Residue 704 [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]
PDB7lw3 A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
Y30 Y132 K137 K170 H174 S202
Binding residue
(residue number reindexed from 1)
Y30 Y132 K137 K170 H174 S202
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
2.1.1.57: methyltransferase cap1.
2.7.7.48: RNA-directed RNA polymerase.
2.7.7.50: mRNA guanylyltransferase.
3.1.13.-
3.4.19.12: ubiquitinyl hydrolase 1.
3.4.22.-
3.4.22.69: SARS coronavirus main proteinase.
3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
4.6.1.-
Gene Ontology
Molecular Function
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:7lw3, PDBe:7lw3, PDBj:7lw3
PDBsum7lw3
PubMed34078893
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]