Structure of PDB 5wkm Chain A Binding Site BS01

Receptor Information
>5wkm Chain A (length=301) Species: 1335626 (Middle East respiratory syndrome-related coronavirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPQLS
DPNYDALLISMTNHSFSVQKHIANLRVVGHAMQGTLLKLTVDVANPSTPA
YTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGY
TKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYC
SVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDM
LAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGV
V
Ligand information
Ligand IDN02
InChIInChI=1S/C26H46N4O10S/c1-7-26(9-12-30(13-10-26)24(35)40-25(4,5)6)39-23(34)29-18(14-16(2)3)21(32)28-19(22(33)41(36,37)38)15-17-8-11-27-20(17)31/h16-19,22,33H,7-15H2,1-6H3,(H,27,31)(H,28,32)(H,29,34)(H,36,37,38)/t17-,18-,19-,22-/m0/s1
InChIKeyXQPCHNVZRFSEQT-OZIGNCPNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC1(CCN(CC1)C(=O)OC(C)(C)C)OC(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
OpenEye OEToolkits 2.0.6CCC1(CCN(CC1)C(=O)OC(C)(C)C)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)S(=O)(=O)O
ACDLabs 12.01C(=O)(NC(C(=O)NC(C(O)S(=O)(=O)O)CC1CCNC1=O)CC(C)C)OC2(CCN(CC2)C(=O)OC(C)(C)C)CC
CACTVS 3.385CCC1(CCN(CC1)C(=O)OC(C)(C)C)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O
OpenEye OEToolkits 2.0.6CCC1(CCN(CC1)C(=O)OC(C)(C)C)OC(=O)NC(CC(C)C)C(=O)NC(CC2CCNC2=O)C(O)S(=O)(=O)O
FormulaC26 H46 N4 O10 S
Name(1S,2S)-2-{[N-({[1-(tert-butoxycarbonyl)-4-ethylpiperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid;
bound form
ChEMBL
DrugBank
ZINC
PDB chain5wkm Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5wkm Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		F143 C148 H166 Q167 M168 E169 D190
Binding residue
(residue number reindexed from 1)		F140 C145 H163 Q164 M165 E166 D187
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.12,IC50=7.5uM
Enzymatic activity
Enzyme Commision number 2.7.7.50: mRNA guanylyltransferase.
3.4.19.12: ubiquitinyl hydrolase 1.
3.4.22.-
3.4.22.69: SARS coronavirus main proteinase.
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5wkm, PDBe:5wkm, PDBj:5wkm
PDBsum5wkm
PubMed29544147
UniProtK9N638|R1A_MERS1 Replicase polyprotein 1a (Gene Name=1a)

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