Structure of PDB 9azx Chain A Binding Site BS01

Receptor Information
>9azx Chain A (length=167) 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
LAVFDKNLYDKLVSSFL
Ligand information
Ligand IDA1AH3
InChIInChI=1S/C17H23N5O14P2/c18-5-17(10-2-1-7-15(19)20-6-21-22(7)10)14(26)12(24)9(35-17)4-33-38(30,31)36-37(28,29)32-3-8-11(23)13(25)16(27)34-8/h1-2,6,8-9,11-14,16,23-27H,3-4H2,(H,28,29)(H,30,31)(H2,19,20,21)/t8-,9-,11-,12-,13-,14-,16-,17+/m1/s1
InChIKeyOXUMWBCVIOHGKL-AFOAYCNSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(n2c1c(ncn2)N)[C@]3([C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)C#N
OpenEye OEToolkits 2.0.7c1cc(n2c1c(ncn2)N)C3(C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)C#N
CACTVS 3.385Nc1ncnn2c1ccc2[C@@]3(O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O)C#N
CACTVS 3.385Nc1ncnn2c1ccc2[C]3(O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O)C#N
ACDLabs 12.01OC1C(O)C(O)OC1COP(=O)(O)OP(=O)(O)OCC1OC(C#N)(C(O)C1O)c1ccc2c(N)ncnn21
FormulaC17 H23 N5 O14 P2
Name{(2R,3S,4R,5R)-5-[(8S)-4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl]-5-cyano-3,4-dihydroxyoxolan-2-yl}methyl [(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl dihydrogen diphosphate
ChEMBL
DrugBank
ZINC
PDB chain9azx Chain A Residue 201 [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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PDB9azx GS-441524-Diphosphate-Ribose Derivatives as Nanomolar Binders and Fluorescence Polarization Tracers for SARS-CoV-2 and Other Viral Macrodomains.
Resolution1.395 Å
Binding residue
(original residue number in PDB)
D22 I23 A38 N40 G46 G48 V49 A50 L126 S128 A129 G130 I131 F132 A154 V155 F156 D157
Binding residue
(residue number reindexed from 1)
D20 I21 A36 N38 G44 G46 V47 A48 L124 S126 A127 G128 I129 F130 A152 V153 F154 D155
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.-
External links
PDB RCSB:9azx, PDBe:9azx, PDBj:9azx
PDBsum9azx
PubMed38646883
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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