Structure of PDB 2zu3 Chain A Binding Site BS01

Receptor Information

>2zu3 Chain A (length=180) Species: 12072 (Coxsackievirus B3)

GPAFEFAVAMMKRNSSTVKTEYGEFTMLGIYDRWAVLPRHAKPGPTILMN
DQEVGVLDAKELVDKDGTNLELTLLKLNRNEKFRDIRGFLAKEEVEVNEA
VLAINTSKFPNMYIPVGQVTEYGFLNLGGTPTKRMLMYNFPTRAGQCGGV
LMSTGKVLGIHVGGNGHQGFSAALLKHYFN

Ligand information

• Ligand ID: ZU3
• InChI: InChI=1S/C32H49N5O7/c1-20(2)16-25(28(40)35-24(13-12-21(3)38)17-23-14-15-33-27(23)39)36-29(41)26(18-34-30(42)32(4,5)6)37-31(43)44-19-22-10-8-7-9-11-22/h7-11,20,23-26H,12-19H2,1-6H3,(H,33,39)(H,34,42)(H,35,40)(H,36,41)(H,37,43)/t23-,24+,25-,26-/m0/s1
• InChIKey: IEQRDAZPCPYZAJ-QYOOZWMWSA-N
• SMILES:
  ACDLabs 12.01: O=C(OCc1ccccc1)NC(C(=O)NC(C(=O)NC(CC2C(=O)NCC2)CCC(=O)C)CC(C)C)CNC(=O)C(C)(C)C
  OpenEye OEToolkits 1.7.0: CC(C)CC(C(=O)NC(CCC(=O)C)CC1CCNC1=O)NC(=O)C(CNC(=O)C(C)(C)C)NC(=O)OCc2ccccc2
  CACTVS 3.370: CC(C)C[CH](NC(=O)[CH](CNC(=O)C(C)(C)C)NC(=O)OCc1ccccc1)C(=O)N[CH](CCC(C)=O)C[CH]2CCNC2=O
  CACTVS 3.370: CC(C)C[C@H](NC(=O)[C@H](CNC(=O)C(C)(C)C)NC(=O)OCc1ccccc1)C(=O)N[C@H](CCC(C)=O)C[C@@H]2CCNC2=O
  OpenEye OEToolkits 1.7.0: CC(C)C[C@@H](C(=O)N[C@H](CCC(=O)C)C[C@@H]1CCNC1=O)NC(=O)[C@H](CNC(=O)C(C)(C)C)NC(=O)OCc2ccccc2
• Formula: C32 H49 N5 O7
• Name: N-[(benzyloxy)carbonyl]-3-[(2,2-dimethylpropanoyl)amino]-L-alanyl-N-[(1R)-4-oxo-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}pentyl]-L-leucinamide;
  TG-0204998
• ZINC: ZINC000058649879
• PDB chain: 2zu3 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2zu3 Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): H40 E71 L127 G128 T142 A144 G145 C147 H161 V162 G163 G164 N165
• Binding residue (residue number reindexed from 1): H40 E71 L127 G128 T142 A144 G145 C147 H161 V162 G163 G164 N165
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.10,Ki=0.8uM

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:2zu3, PDBe:2zu3, PDBj:2zu3
• PDBsum: 2zu3
• PubMed: 19144641
• UniProt: P03313|POLG_CXB3N Genome polyprotein