Structure of PDB 6vgz Chain A Binding Site BS01

Receptor Information

>6vgz Chain A (length=296) Species: 1335626 (Middle East respiratory syndrome-related coronavirus)

HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQ
LSDPNYDALLISMTNHSFSVQKHLRVVGHAMQGTLLKLTVDVANPSTPAY
TFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYT
KEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCS
VNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDML
AVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQI

Ligand information

• Ligand ID: QZG
• InChI: InChI=1S/C23H41N3O5/c1-14(2)11-20(22(29)25-18(13-27)12-17-9-10-24-21(17)28)26-23(30)31-19-7-5-16(6-8-19)15(3)4/h14-20,27H,5-13H2,1-4H3,(H,24,28)(H,25,29)(H,26,30)/t16-,17-,18-,19-,20-/m0/s1
• InChIKey: SPCFKQMKRNNPLF-HVTWWXFQSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)CO)NC(=O)OC2CCC(CC2)C(C)C
  ACDLabs 12.01: C(=O)(NC(CC(C)C)C(NC(CC1C(=O)NCC1)CO)=O)OC2CCC(CC2)C(C)C
  CACTVS 3.385: CC(C)C[CH](NC(=O)O[CH]1CC[CH](CC1)C(C)C)C(=O)N[CH](CO)C[CH]2CCNC2=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)CO)NC(=O)OC2CCC(CC2)C(C)C
  CACTVS 3.385: CC(C)C[C@H](NC(=O)O[C@H]1CC[C@@H](CC1)C(C)C)C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
• Formula: C23 H41 N3 O5
• Name: N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[trans-4-(propan-2-yl)cyclohexyl]oxy}carbonyl)-L-leucinamide
• PDB chain: 6vgz Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vgz 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): F143 C148 Q167 M168 E169 D190 K191 Q192
• Binding residue (residue number reindexed from 1): F139 C144 Q163 M164 E165 D186 K187 Q188
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.57: methyltransferase cap1.
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:6vgz, PDBe:6vgz, PDBj:6vgz
• PDBsum: 6vgz
• PubMed: 32747425
• UniProt: T2B9U0