Structure of PDB 5trf Chain B Binding Site BS01

Receptor Information
>5trf Chain B (length=100) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQ
YIMTKRLYQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQ
Ligand information
Ligand ID7HC
InChIInChI=1S/C29H34Cl2FN3O3/c1-28(2,3)14-22-29(19-12-7-15(30)13-21(19)34-27(29)38)23(18-5-4-6-20(31)24(18)32)25(35-22)26(37)33-16-8-10-17(36)11-9-16/h4-7,12-13,16-17,22-23,25,35-36H,8-11,14H2,1-3H3,(H,33,37)(H,34,38)/t16-,17-,22-,23-,25+,29+/m0/s1
InChIKeyIDKAKZRYYDCJDU-HBMMIIHUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)(C)CC1C2(c3ccc(cc3NC2=O)Cl)C(C(N1)C(=O)NC4CCC(CC4)O)c5cccc(c5F)Cl
ACDLabs 12.01O=C5C3(C(c1c(F)c(ccc1)Cl)C(C(NC2CCC(O)CC2)=O)NC3CC(C)(C)C)c4c(cc(cc4)Cl)N5
CACTVS 3.385CC(C)(C)C[CH]1N[CH]([CH](c2cccc(Cl)c2F)[C]13C(=O)Nc4cc(Cl)ccc34)C(=O)N[CH]5CC[CH](O)CC5
OpenEye OEToolkits 2.0.6CC(C)(C)C[C@H]1[C@]2(c3ccc(cc3NC2=O)Cl)[C@H]([C@@H](N1)C(=O)NC4CCC(CC4)O)c5cccc(c5F)Cl
CACTVS 3.385CC(C)(C)C[C@@H]1N[C@H]([C@H](c2cccc(Cl)c2F)[C@]13C(=O)Nc4cc(Cl)ccc34)C(=O)N[C@@H]5CC[C@@H](O)CC5
FormulaC29 H34 Cl2 F N3 O3
Name(2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide
ChEMBLCHEMBL2381408
DrugBankDB12541
ZINCZINC000145424989
PDB chain5trf Chain B Residue 201 [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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PDB5trf SAR405838: an optimized inhibitor of MDM2-p53 interaction that induces complete and durable tumor regression.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		V14 T16 L54 L57 G58 I61 M62 Y67 F86 V93 H96 I99 Y100
Binding residue
(residue number reindexed from 1)		V5 T7 L45 L48 G49 I52 M53 Y58 F74 V81 H84 I87 Y88
Annotation score1
Binding affinityMOAD: Ki=0.88nM
BindingDB: Ki=0.880000nM,Kd=2.7nM
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

View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:5trf, PDBe:5trf, PDBj:5trf
PDBsum5trf
PubMed25145672
UniProtQ00987|MDM2_HUMAN E3 ubiquitin-protein ligase Mdm2 (Gene Name=MDM2)

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