Structure of PDB 7d4f Chain A Binding Site BS01

Receptor Information
>7d4f Chain A (length=898) 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]
SFLNRVCGVSAARLTPCVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDD
NLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIMVPHISR
QRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFV
ENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW
YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYI
KWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVL
FSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRL
SFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFN
KDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDI
RQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYY
DSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTM
TNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMG
WDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEM
VMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIA
DKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCF
NSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQH
TMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDA
YPLTKHPNQEYADVFHLYLQYIRKLHDELNTSRYWEPEFYEAMYTPHT
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain7d4f Chain A Residue 1001 [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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PDB7d4f Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin.
Resolution2.57 Å
Binding residue
(original residue number in PDB)		H295 C301 C306 C310
Binding residue
(residue number reindexed from 1)		H279 C285 C290 C294
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:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005524 ATP binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7d4f, PDBe:7d4f, PDBj:7d4f
PDBsum7d4f
PubMed33674802
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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