Structure of PDB 8rzc Chain A Binding Site BS01

Receptor Information
>8rzc Chain A (length=296) 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]
SQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLC
QYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLN
DFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFT
YICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASS
SEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFP
LKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVN
Ligand information
Ligand IDA1H4D
InChIInChI=1S/C21H21N7O5S/c22-18-15-19(25-8-24-18)28(10-26-15)20-17(30)16(29)14(33-20)7-34-6-11-3-12(21(31)32)5-13(4-11)27-2-1-23-9-27/h1-5,8-10,14,16-17,20,29-30H,6-7H2,(H,31,32)(H2,22,24,25)
InChIKeyYCJODFCZOYGSRH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CSCc4cc(cc(c4)C(O)=O)n5ccnc5)[CH](O)[CH]3O
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCc4cc(cc(c4)C(O)=O)n5ccnc5)[C@H](O)[C@@H]3O
OpenEye OEToolkits 2.0.7c1cn(cn1)c2cc(cc(c2)C(=O)O)CSC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O
OpenEye OEToolkits 2.0.7c1cn(cn1)c2cc(cc(c2)C(=O)O)CSCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
FormulaC21 H21 N7 O5 S
Name3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-imidazol-1-yl-benzoic acid;
3-(((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)methyl)-5-(1H-imidazol-1-yl)benzoic acid
ChEMBL
DrugBank
ZINC
PDB chain8rzc Chain A Residue 302 [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]
PDB8rzc Towards automated crystallographic structure refinement with phenix.refine.
Resolution2.35 Å
Binding residue
(original residue number in PDB)
G71 G73 D99 L100 C115 M131 Y132 P134 F149
Binding residue
(residue number reindexed from 1)
G70 G72 D98 L99 C114 M130 Y131 P133 F148
Annotation score2
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:8rzc, PDBe:8rzc, PDBj:8rzc
PDBsum8rzc
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]