Structure of PDB 1cqq Chain A Binding Site BS01

Receptor Information

>1cqq Chain A (length=180) Species: 12130 (rhinovirus A2)

GPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQVD
GITTKVIDSYDLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYPNC
NLALLANQPEPTIINVGDVVSYGNILLSGNQTARMLKYSYPTKSGYCGGV
LYKIGQVLGIHVGGNGRDGFSAMLLRSYFT

Ligand information

• Ligand ID: AG7
• InChI: InChI=1S/C31H41FN4O7/c1-5-42-27(38)11-10-24(16-21-12-13-33-29(21)39)34-30(40)22(15-20-6-8-23(32)9-7-20)17-26(37)28(18(2)3)35-31(41)25-14-19(4)43-36-25/h6-9,14,18,21-22,24,28H,5,10-13,15-17H2,1-4H3,(H,33,39)(H,34,40)(H,35,41)/t21-,22+,24+,28-/m0/s1
• InChIKey: LMIUALQNZXJHOG-IFILWLFVSA-N
• SMILES:
  ACDLabs 12.01: O=C(NC(C(=O)CC(C(=O)NC(CC1C(=O)NCC1)CCC(=O)OCC)Cc2ccc(F)cc2)C(C)C)c3noc(c3)C
  CACTVS 3.370: CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC(=O)[CH](NC(=O)c2cc(C)on2)C(C)C)Cc3ccc(F)cc3
  OpenEye OEToolkits 1.7.2: CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccc(cc2)F)CC(=O)C(C(C)C)NC(=O)c3cc(on3)C
  CACTVS 3.370: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H](CC(=O)[C@@H](NC(=O)c2cc(C)on2)C(C)C)Cc3ccc(F)cc3
  OpenEye OEToolkits 1.7.2: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccc(cc2)F)CC(=O)[C@H](C(C)C)NC(=O)c3cc(on3)C
• Formula: C31 H41 F N4 O7
• Name: 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER;
  RUPINTRIVIR, bound form
• ZINC: ZINC000014880293
• PDB chain: 1cqq Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1cqq Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): F25 H40 E71 L127 S128 T142 S144 G145 C147 H161 V162 G163 G164 N165 F170
• Binding residue (residue number reindexed from 1): F25 H40 E71 L127 S128 T142 S144 G145 C147 H161 V162 G163 G164 N165 F170
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H40 E71 G145 C147
• Catalytic site (residue number reindexed from 1): H40 E71 G145 C147
• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.22.28: picornain 3C.
  3.4.22.29: picornain 2A.
  3.6.1.15: nucleoside-triphosphate phosphatase.

Gene Ontology

Molecular Function

• GO:0004197 cysteine-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:1cqq, PDBe:1cqq, PDBj:1cqq
• PDBsum: 1cqq
• PubMed: 10500114
• UniProt: P04936|POLG_HRV2 Genome polyprotein