Structure of PDB 5l69 Chain V Binding Site BS02

Receptor Information

>5l69 Chain V (length=226) Species: 559292 (Saccharomyces cerevisiae S288C)

TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAA
DTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIV
AGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEE
AIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQ
KSYKFPRGTTAVLKESIVNICDIQEE

Ligand information

• Ligand ID: 79P
• InChI: InChI=1S/C32H43N5O6/c1-21(20-38)30(40)27(16-23-8-4-3-5-9-23)35-32(42)28(17-24-18-33-26-11-7-6-10-25(24)26)36-31(41)22(2)34-29(39)19-37-12-14-43-15-13-37/h3-11,18,21-22,27-28,30,33,38,40H,12-17,19-20H2,1-2H3,(H,34,39)(H,35,42)(H,36,41)/t21-,22-,27+,28+,30+/m1/s1
• InChIKey: OMCVZYCNWOQLDV-WZPPRZIKSA-N
• SMILES:
  CACTVS 3.385: C[CH](CO)[CH](O)[CH](Cc1ccccc1)NC(=O)[CH](Cc2c[nH]c3ccccc23)NC(=O)[CH](C)NC(=O)CN4CCOCC4
  CACTVS 3.385: C[C@H](CO)[C@H](O)[C@H](Cc1ccccc1)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@@H](C)NC(=O)CN4CCOCC4
  OpenEye OEToolkits 2.0.5: CC(CO)C(C(Cc1ccccc1)NC(=O)C(Cc2c[nH]c3c2cccc3)NC(=O)C(C)NC(=O)CN4CCOCC4)O
  OpenEye OEToolkits 2.0.5: C[C@H](CO)[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](Cc2c[nH]c3c2cccc3)NC(=O)[C@@H](C)NC(=O)CN4CCOCC4)O
• Formula: C32 H43 N5 O6
• Name: (2~{S})-3-(1~{H}-indol-3-yl)-~{N}-[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]-2-[[(2~{R})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide
• ZINC: ZINC000584905109
• PDB chain: 5l69 Chain V Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l69 A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): T1 S20 T21 C31 K33 A46 G47 T48 A49 G168
• Binding residue (residue number reindexed from 1): T1 S20 T21 C31 K33 A46 G47 T48 A49 G168
• Annotation score: 1

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 S129 D166 S169
• 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:5l69, PDBe:5l69, PDBj:5l69
• PDBsum: 5l69
• PubMed: 27789522
• UniProt: P25043|PSB2_YEAST Proteasome subunit beta type-2 (Gene Name=PUP1)