Structure of PDB 6z72 Chain B Binding Site BS01

Receptor Information
>6z72 Chain B (length=173) 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]
VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFLEMKSEK
Ligand information
Ligand IDA3R
InChIInChI=1S/C15H24N6O11P2/c16-13-10-14(19-5-18-13)21(6-20-10)15-12(24)11(23)9(31-15)4-30-34(27,28)32-33(25,26)29-3-7-1-8(22)2-17-7/h5-9,11-12,15,17,22-24H,1-4H2,(H,25,26)(H,27,28)(H2,16,18,19)/t7-,8+,9+,11+,12+,15+/m0/s1
InChIKeyPHEYQOBMMIEFLO-IBCGMDAMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4C[C@H](CN4)O)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4C[CH](O)CN4)[CH](O)[CH]3O
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4CC(CN4)O)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H]4C[C@@H](O)CN4)[C@@H](O)[C@H]3O
FormulaC15 H24 N6 O11 P2
Name Adenosine Diphosphate (Hydroxymethyl)pyrrolidine monoalcohol
ChEMBL
DrugBank
ZINCZINC000049785398
PDB chain6z72 Chain B Residue 401 [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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PDB6z72 Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D226 I227 A242 N244 G251 G252 V253 L330 S332 A333 G334 I335 F336 A358 F360
Binding residue
(residue number reindexed from 1)		D20 I21 A36 N38 G45 G46 V47 L124 S126 A127 G128 I129 F130 A152 F154
Annotation score3
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.-
External links
PDB RCSB:6z72, PDBe:6z72, PDBj:6z72
PDBsum6z72
PubMed33202171
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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