Structure of PDB 4qlu Chain K Binding Site BS02

Receptor Information

>4qlu Chain K (length=212) Species: 559292 (Saccharomyces cerevisiae S288C)

TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAA
DCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTM
ICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSV
EDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKV
KEEEGSFNNVIG

Ligand information

• Ligand ID: 38X
• InChI: InChI=1S/C37H46N4O5/c1-22(21-42)34(43)32(17-25-11-5-4-6-12-25)40-37(46)33(19-27-20-38-31-16-10-9-15-29(27)31)41-35(44)24(3)39-36(45)30-18-26-13-7-8-14-28(26)23(30)2/h7-10,13-16,20,22,24-25,32-33,38,42H,4-6,11-12,17-19,21H2,1-3H3,(H,39,45)(H,40,46)(H,41,44)/t22-,24-,32+,33+/m1/s1
• InChIKey: WFCYBAJFPAJLJW-BVZMXYCPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC1=C(Cc2c1cccc2)C(=O)NC(C)C(=O)NC(Cc3c[nH]c4c3cccc4)C(=O)NC(CC5CCCCC5)C(=O)C(C)CO
  ACDLabs 12.01: O=C(C(C)CO)C(NC(=O)C(NC(=O)C(NC(=O)C2=C(c1ccccc1C2)C)C)Cc4c3ccccc3nc4)CC5CCCCC5
  OpenEye OEToolkits 1.7.6: CC1=C(Cc2c1cccc2)C(=O)N[C@H](C)C(=O)N[C@@H](Cc3c[nH]c4c3cccc4)C(=O)N[C@@H](CC5CCCCC5)C(=O)[C@H](C)CO
  CACTVS 3.385: C[CH](CO)C(=O)[CH](CC1CCCCC1)NC(=O)[CH](Cc2c[nH]c3ccccc23)NC(=O)[CH](C)NC(=O)C4=C(C)c5ccccc5C4
  CACTVS 3.385: C[C@H](CO)C(=O)[C@H](CC1CCCCC1)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@@H](C)NC(=O)C4=C(C)c5ccccc5C4
• Formula: C37 H46 N4 O5
• Name: N-[(3-methyl-1H-inden-2-yl)carbonyl]-D-alanyl-N-[(2S,4R)-1-cyclohexyl-5-hydroxy-4-methyl-3-oxopentan-2-yl]-L-tryptophanamide
• ZINC: ZINC000098208410
• PDB chain: 4qlu Chain K Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4qlu Structure-based design of beta 1i or beta 5i specific inhibitors of human immunoproteasomes
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): T1 R19 A20 T21 G47 G48 A49 Y170
• Binding residue (residue number reindexed from 1): T1 R19 A20 T21 G47 G48 A49 Y170
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.08,IC50=8.3nM

Enzymatic activity

• Catalytic site (original residue number in PDB): T1 D17 R19 K33 G47 S131 D168 S171
• 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:4qlu, PDBe:4qlu, PDBj:4qlu
• PDBsum: 4qlu
• PubMed: 25006746
• UniProt: P30656|PSB5_YEAST Proteasome subunit beta type-5 (Gene Name=PRE2)