Structure of PDB 7d4f Chain A Binding Site BS03

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 1003 [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)		N496 N497 K500 R569 Q573 K577 G590 A685 L758
Binding residue
(residue number reindexed from 1)		N480 N481 K484 R553 Q557 K561 G574 A669 L742
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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