Structure of PDB 2xyr Chain A Binding Site BS01

Receptor Information
>2xyr Chain A (length=286) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQ
YLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLND
FVSDADSTLIGDCATVHTANKWDLIISDMYDPRTKENDSKEGFFTYLCGF
IKQKLALGGSIAVKITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFL
IGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRG
TAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSS
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain2xyr Chain A Residue 1298 [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]
PDB2xyr Crystal Structure and Functional Analysis of the Sars-Coronavirus RNA CAP 2'-O-Methyltransferase Nsp10/Nsp16 Complex.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N43 G71 G73 P80 G81 D99 L100 C115 D130 M131 Y132
Binding residue
(residue number reindexed from 1)		N41 G69 G71 P78 G79 D97 L98 C113 D128 M129 Y130
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.13,IC50=0.74uM
Enzymatic activity
Enzyme Commision number 2.1.1.-
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:2xyr, PDBe:2xyr, PDBj:2xyr
PDBsum2xyr
PubMed21637813
UniProtP0C6X7|R1AB_SARS Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]