Structure of PDB 9atf Chain A Binding Site BS01

Receptor Information

>9atf Chain A (length=305) Species: 1335626 (Middle East respiratory syndrome-related coronavirus)

HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQ
LSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVAN
PSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSC
GSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQL
TDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGT
QSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNM
QIMGV

Ligand information

• Ligand ID: A1AGP
• InChI: InChI=1S/C26H42F2N4O9S/c1-15(2)11-19(23(35)30-20(24(36)42(38,39)40)12-17-7-10-29-22(17)34)31-25(37)41-14-18-3-4-21(33)32(18)13-16-5-8-26(27,28)9-6-16/h15-20,24,36H,3-14H2,1-2H3,(H,29,34)(H,30,35)(H,31,37)(H,38,39,40)/t17-,18-,19-,20-,24-/m0/s1
• InChIKey: RHYSFFXFVGVALZ-HPGFDKJQSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC[CH]1CCC(=O)N1CC2CCC(F)(F)CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC[C@@H]2CCC(=O)N2CC3CCC(CC3)(F)F
  ACDLabs 12.01: O=C1NCCC1CC(NC(=O)C(CC(C)C)NC(=O)OCC1CCC(=O)N1CC1CCC(F)(F)CC1)C(O)S(=O)(=O)O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CCC(=O)N2CC3CCC(CC3)(F)F
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC[C@@H]1CCC(=O)N1CC2CCC(F)(F)CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S](O)(=O)=O
• Formula: C26 H42 F2 N4 O9 S
• Name: (1S,2S)-2-({N-[({(2S)-1-[(4,4-difluorocyclohexyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 9atf Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9atf Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): F143 G146 C148 H166 Q167 M168 E169 D190 Q192 H194
• Binding residue (residue number reindexed from 1): F145 G148 C150 H168 Q169 M170 E171 D192 Q194 H196
• Annotation score: 1

External links

• PDB: RCSB:9atf, PDBe:9atf, PDBj:9atf
• PDBsum: 9atf
• PubMed: 38953866
• UniProt: K9N638|R1A_MERS1 Replicase polyprotein 1a (Gene Name=1a)