Structure of PDB 2amd Chain B Binding Site BS01

Receptor Information
>2amd Chain B (length=304) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAED
MLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKT
PKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSV
GFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDT
TITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVD
ILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVR
QCSG
Ligand information
Ligand ID9IN
InChIInChI=1S/C32H49N5O8/c1-8-45-25(38)10-9-23(16-21-11-13-33-28(21)39)34-30(41)24(15-18(2)3)35-31(42)26(19(4)5)37-32(43)27(20(6)7)36-29(40)22-12-14-44-17-22/h9-10,12,14,17-21,23-24,26-27H,8,11,13,15-16H2,1-7H3,(H,33,39)(H,34,41)(H,35,42)(H,36,40)(H,37,43)/b10-9+/t21-,23+,24-,26-,27-/m0/s1
InChIKeyJQGYBVLTABWBOF-VTQXMFKGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCOC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](C(C)C)NC(=O)[C@H](C(C)C)NC(=O)c2ccoc2
CACTVS 3.341CCOC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC(C)C)NC(=O)[CH](NC(=O)[CH](NC(=O)c2cocc2)C(C)C)C(C)C
CACTVS 3.341CCOC(=O)/C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)c2cocc2)C(C)C)C(C)C
ACDLabs 10.04O=C(NC(C(=O)NC(C(=O)NC(C(=O)NC(\C=C\C(=O)OCC)CC1C(=O)NCC1)CC(C)C)C(C)C)C(C)C)c2ccoc2
OpenEye OEToolkits 1.5.0CCOC(=O)C=CC(CC1CCNC1=O)NC(=O)C(CC(C)C)NC(=O)C(C(C)C)NC(=O)C(C(C)C)NC(=O)c2ccoc2
FormulaC32 H49 N5 O8
NameN-(3-FUROYL)-D-VALYL-L-VALYL-N~1~-((1R,2Z)-4-ETHOXY-4-OXO-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-D-LEUCINAMIDE;
(E)-(4S,6S)-6-((S)-2-{(S)-2-[(FURAN-2-CARBONYL)-AMINO]-3-METHYL-BUTYRYLAMINO}-3-METHYL-BUTYRYLAMINO)-8-METHYL-5-OXO-4-((R)-2-OXO-PYRROLIDIN-3-YLMETHYL)-NON-2-ENOIC ACID ETHYL ESTER
ChEMBL
DrugBankDB04613
ZINCZINC000014881283
PDB chain2amd Chain B Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2amd Design of Wide-Spectrum Inhibitors Targeting Coronavirus Main Proteases.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		T26 N142 G143 C145 H163 H164 M165 E166 P168 R188 Q189 T190 A191
Binding residue
(residue number reindexed from 1)		T28 N144 G145 C147 H165 H166 M167 E168 P170 R190 Q191 T192 A193
Annotation score1
Binding affinityBindingDB: Ki=6700nM
Enzymatic activity
Catalytic site (original residue number in PDB) H41 G143 C145
Catalytic site (residue number reindexed from 1) H43 G145 C147
Enzyme Commision number 2.1.1.-
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:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2amd, PDBe:2amd, PDBj:2amd
PDBsum2amd
PubMed16128623
UniProtP0C6X7|R1AB_SARS Replicase polyprotein 1ab (Gene Name=rep)

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