Structure of PDB 3vbg Chain B Binding Site BS02

Receptor Information
>3vbg Chain B (length=85) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHI
VYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV
Ligand information
Ligand ID03M
InChIInChI=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-
InChIKeyOEXMEVPQEPHTAQ-IDUWFGFVSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc1ccc2c(c1C)ncc2/C=C3/C(=O)N(C(=O)N3)Cc4cc(F)c(F)cc4
OpenEye OEToolkits 1.7.2Cc1c(ccc2c1[nH]cc2C=C3C(=O)N(C(=O)N3)Cc4ccc(c(c4)F)F)Cl
CACTVS 3.370Cc1c(Cl)ccc2c(c[nH]c12)C=C3NC(=O)N(Cc4ccc(F)c(F)c4)C3=O
CACTVS 3.370Cc1c(Cl)ccc2c(c[nH]c12)\C=C3/NC(=O)N(Cc4ccc(F)c(F)c4)C3=O
OpenEye OEToolkits 1.7.2Cc1c(ccc2c1[nH]cc2/C=C\3/C(=O)N(C(=O)N3)Cc4ccc(c(c4)F)F)Cl
FormulaC20 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
ChEMBLCHEMBL5267044
DrugBank
ZINCZINC000098207755
PDB chain3vbg Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3vbg Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		I61 M62 Y67 Q72
Binding residue
(residue number reindexed from 1)		I37 M38 Y43 Q48
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.48,IC50=33nM
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

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Biological Process
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Cellular Component
External links
PDB RCSB:3vbg, PDBe:3vbg, PDBj:3vbg
PDBsum3vbg
PubMed22745160
UniProtQ00987|MDM2_HUMAN E3 ubiquitin-protein ligase Mdm2 (Gene Name=MDM2)

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