Structure of PDB 3mg6 Chain K Binding Site BS02

Receptor Information

>3mg6 Chain K (length=212) Species: 4932 (Saccharomyces cerevisiae)

TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAA
DCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTM
ICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSV
EDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKV
KEEEGSFNNVIG

Ligand information

• Ligand ID: LZT
• InChI: InChI=1S/C34H39N3O6/c1-21-9-11-24(12-10-21)20-35-33(41)29(16-13-23-7-5-4-6-8-23)36-34(42)32(22(2)38)37-31(40)18-25-17-30(39)27-15-14-26(43-3)19-28(25)27/h4-12,14-15,19,22,25,29,32,38H,13,16-18,20H2,1-3H3,(H,35,41)(H,36,42)(H,37,40)/t22-,25+,29+,32+/m1/s1
• InChIKey: XTNVDVZDMWYKHD-TWQSKLGKSA-N
• SMILES:
  CACTVS 3.370: COc1ccc2C(=O)C[C@@H](CC(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@@H](CCc3ccccc3)C(=O)NCc4ccc(C)cc4)c2c1
  OpenEye OEToolkits 1.7.0: Cc1ccc(cc1)CNC(=O)[C@H](CCc2ccccc2)NC(=O)[C@H]([C@@H](C)O)NC(=O)C[C@@H]3CC(=O)c4c3cc(cc4)OC
  ACDLabs 12.01: O=C(NCc1ccc(cc1)C)C(NC(=O)C(NC(=O)CC3c2cc(OC)ccc2C(=O)C3)C(O)C)CCc4ccccc4
  OpenEye OEToolkits 1.7.0: Cc1ccc(cc1)CNC(=O)C(CCc2ccccc2)NC(=O)C(C(C)O)NC(=O)CC3CC(=O)c4c3cc(cc4)OC
  CACTVS 3.370: COc1ccc2C(=O)C[CH](CC(=O)N[CH]([CH](C)O)C(=O)N[CH](CCc3ccccc3)C(=O)NCc4ccc(C)cc4)c2c1
• Formula: C34 H39 N3 O6
• Name: N~2~-{[(1S)-6-methoxy-3-oxo-2,3-dihydro-1H-inden-1-yl]acetyl}-N-{(1S)-1-[(4-methylbenzyl)carbamoyl]-3-phenylpropyl}-L-threoninamide
• ZINC: ZINC000064527172
• PDB chain: 3mg6 Chain K Residue 213

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mg6 Characterization of a new series of non-covalent proteasome inhibitors with exquisite potency and selectivity for the 20S beta5-subunit.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): A20 T21 V31 K33 M45 G47 G48 A49 S96
• Binding residue (residue number reindexed from 1): A20 T21 V31 K33 M45 G47 G48 A49 S96
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.89,Ki=13nM

Enzymatic activity

• Catalytic site (original residue number in PDB): T1 D17 R19 K33 G47 S129 D166 S169
• Catalytic site (residue number reindexed from 1): T1 D17 R19 K33 G47 S131 D168 S171
• Enzyme Commision number: 3.4.25.1: proteasome endopeptidase complex.

Gene Ontology

Molecular Function

• GO:0004298 threonine-type endopeptidase activity

Biological Process

• GO:0051603 proteolysis involved in protein catabolic process

Cellular Component

• GO:0005839 proteasome core complex

External links

• PDB: RCSB:3mg6, PDBe:3mg6, PDBj:3mg6
• PDBsum: 3mg6
• PubMed: 20632995
• UniProt: P30656|PSB5_YEAST Proteasome subunit beta type-5 (Gene Name=PRE2)