Structure of PDB 6xk9 Chain X Binding Site BS01

Receptor Information

>6xk9 Chain X (length=196) Species: 9606 (Homo sapiens)

GPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSD
DVETDTVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVI
IEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQ
DQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLV

Ligand information

• Ligand ID: V4M
• InChI: InChI=1S/C22H18ClF2N3O4/c23-15-4-2-14(3-5-15)22(24,25)21(32)26-10-12-1-6-16-13(9-12)11-28(20(16)31)17-7-8-18(29)27-19(17)30/h1-6,9,17H,7-8,10-11H2,(H,26,32)(H,27,29,30)/t17-/m0/s1
• InChIKey: PWBHUSLMHZLGRN-KRWDZBQOSA-N
• SMILES:
  CACTVS 3.385: FC(F)(C(=O)NCc1ccc2c(CN([CH]3CCC(=O)NC3=O)C2=O)c1)c4ccc(Cl)cc4
  OpenEye OEToolkits 2.0.7: c1cc(ccc1C(C(=O)NCc2ccc3c(c2)CN(C3=O)C4CCC(=O)NC4=O)(F)F)Cl
  ACDLabs 12.01: c2cc4C(N(C1CCC(NC1=O)=O)Cc4cc2CNC(C(F)(F)c3ccc(cc3)Cl)=O)=O
  OpenEye OEToolkits 2.0.7: c1cc(ccc1C(C(=O)NCc2ccc3c(c2)CN(C3=O)[C@H]4CCC(=O)NC4=O)(F)F)Cl
  CACTVS 3.385: FC(F)(C(=O)NCc1ccc2c(CN([C@H]3CCC(=O)NC3=O)C2=O)c1)c4ccc(Cl)cc4
• Formula: C22 H18 Cl F2 N3 O4
• Name: 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide
• PDB chain: 6xk9 Chain Z Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xk9 CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells.
• Resolution: 3.64 Å
• Binding residue (original residue number in PDB): V535 K571 S573 G574 I625 G626 K627
• Binding residue (residue number reindexed from 1): V99 K135 S137 G138 I189 G190 K191
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

Gene Ontology

Molecular Function

• GO:0005525 GTP binding

External links

• PDB: RCSB:6xk9, PDBe:6xk9, PDBj:6xk9
• PDBsum: 6xk9
• PubMed: 33197925
• UniProt: P15170|ERF3A_HUMAN Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (Gene Name=GSPT1)