Structure of PDB 3vbg Chain C Binding Site BS01

Receptor Information

>3vbg Chain C (length=84) Species: 9606 (Homo sapiens)

TLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIV
YCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV

Ligand information

• Ligand ID: 03M
• InChI: InChI=1S/C20H14ClF2N3O2/c1-10-14(21)4-3-13-12(8-24-18(10)13)7-17-19(27)26(20(28)25-17)9-11-2-5-15(22)16(23)6-11/h2-8,24H,9H2,1H3,(H,25,28)/b17-7-
• InChIKey: OEXMEVPQEPHTAQ-IDUWFGFVSA-N
• SMILES:
  ACDLabs 12.01: Clc1ccc2c(c1C)ncc2/C=C3/C(=O)N(C(=O)N3)Cc4cc(F)c(F)cc4
  OpenEye OEToolkits 1.7.2: Cc1c(ccc2c1[nH]cc2C=C3C(=O)N(C(=O)N3)Cc4ccc(c(c4)F)F)Cl
  CACTVS 3.370: Cc1c(Cl)ccc2c(c[nH]c12)C=C3NC(=O)N(Cc4ccc(F)c(F)c4)C3=O
  CACTVS 3.370: Cc1c(Cl)ccc2c(c[nH]c12)\C=C3/NC(=O)N(Cc4ccc(F)c(F)c4)C3=O
  OpenEye OEToolkits 1.7.2: Cc1c(ccc2c1[nH]cc2/C=C\3/C(=O)N(C(=O)N3)Cc4ccc(c(c4)F)F)Cl
• Formula: C20 H14 Cl F2 N3 O2
• Name: (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione
• ChEMBL: CHEMBL5267044
• ZINC: ZINC000098207755
• PDB chain: 3vbg Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vbg Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): I61 Y67 Q72
• Binding residue (residue number reindexed from 1): I36 Y42 Q47
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.

Gene Ontology

Biological Process

• GO:0043066 negative regulation of apoptotic process
• GO:0051726 regulation of cell cycle

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:3vbg, PDBe:3vbg, PDBj:3vbg
• PDBsum: 3vbg
• PubMed: 22745160
• UniProt: Q00987|MDM2_HUMAN E3 ubiquitin-protein ligase Mdm2 (Gene Name=MDM2)