Structure of PDB 5l60 Chain K Binding Site BS01

Receptor Information

>5l60 Chain K (length=211) Species: 9606,559292

TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAA
DCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTM
ICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVLDSNYKWDLSVE
DALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVK
EEEGSFNNVIG

Ligand information

• Ligand ID: 39V
• InChI: InChI=1S/C37H40N4O5/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/h4-16,20,22,24,32-33,38,42H,17-19,21H2,1-3H3,(H,39,45)(H,40,46)(H,41,44)/t22-,24-,32+,33+/m1/s1
• InChIKey: GCKVAOQLUKFJOV-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
  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
  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
  ACDLabs 12.01: O=C(C(C)CO)C(NC(=O)C(NC(=O)C(NC(=O)C2=C(c1ccccc1C2)C)C)Cc4c3ccccc3nc4)Cc5ccccc5
• Formula: C37 H40 N4 O5
• Name: N-[(3-methyl-1H-inden-2-yl)carbonyl]-D-alanyl-N-[(2S,4R)-5-hydroxy-4-methyl-3-oxo-1-phenylpentan-2-yl]-L-tryptophanamide
• ZINC: ZINC000098208414
• PDB chain: 5l60 Chain K Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l60 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 A20 T21 V31 K33 M45 G47 A49 Y169
• Binding residue (residue number reindexed from 1): T1 A20 T21 V31 K33 M45 G47 A49 Y169
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T1 D17 R19 K33 G47 S130 D167 S170
• Catalytic site (residue number reindexed from 1): T1 D17 R19 K33 G47 S130 D167 S170
• 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:5l60, PDBe:5l60, PDBj:5l60
• PDBsum: 5l60
• PubMed: 27789522
• UniProt: P28074|PSB5_HUMAN Proteasome subunit beta type-5 (Gene Name=PSMB5);
  P30656|PSB5_YEAST Proteasome subunit beta type-5 (Gene Name=PRE2)