Structure of PDB 7d4f Chain A Binding Site BS04

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 IDH3U
InChIInChI=1S/C25H21N3O11S3/c1-13-5-6-15(10-20(13)28-24(29)14-3-2-4-16(26)9-14)25(30)27-19-7-8-21(41(34,35)36)18-11-17(40(31,32)33)12-22(23(18)19)42(37,38)39/h2-12H,26H2,1H3,(H,27,30)(H,28,29)(H,31,32,33)(H,34,35,36)(H,37,38,39)
InChIKeyFWPDBHFZCRXISJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(cc1NC(=O)c2cccc(N)c2)C(=O)Nc3ccc(c4cc(cc(c34)[S](O)(=O)=O)[S](O)(=O)=O)[S](O)(=O)=O
OpenEye OEToolkits 2.0.7Cc1ccc(cc1NC(=O)c2cccc(c2)N)C(=O)Nc3ccc(c4c3c(cc(c4)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O
FormulaC25 H21 N3 O11 S3
Name8-(3-(3-aminobenzamido)-4-methylbenzamido)naphthalene-1,3,5-trisulfonic acid
ChEMBLCHEMBL2009384
DrugBank
ZINCZINC000082186151
PDB chain7d4f Chain A Residue 1004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		H439 S549 A550 R553 R836 D865
Binding residue
(residue number reindexed from 1)		H423 S533 A534 R537 R820 D849
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

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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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