Structure of PDB 6i3s Chain A Binding Site BS01

Receptor Information
>6i3s Chain A (length=94) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLY
DEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Ligand information
Ligand IDH28
InChIInChI=1S/C23H18Cl2FN3O2/c24-12-6-7-14-16(8-12)28-22(31)23(14)19(13-2-1-3-15(25)20(13)26)18-17(9-27-21(18)30)29(23)10-11-4-5-11/h1-3,6-9,11,17-19H,4-5,10H2,(H,28,31)/t17-,18+,19-,23+/m0/s1
InChIKeyZWMAKFAKGSTVDL-QPXQOZNCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1c(Cl)cccc1[CH]2[CH]3[CH](C=NC3=O)N(CC4CC4)[C]25C(=O)Nc6cc(Cl)ccc56
CACTVS 3.385Fc1c(Cl)cccc1[C@H]2[C@H]3[C@H](C=NC3=O)N(CC4CC4)[C@@]25C(=O)Nc6cc(Cl)ccc56
OpenEye OEToolkits 2.0.6c1cc(c(c(c1)Cl)F)[C@H]2[C@H]3[C@H](C=NC3=O)N([C@]24c5ccc(cc5NC4=O)Cl)CC6CC6
OpenEye OEToolkits 2.0.6c1cc(c(c(c1)Cl)F)C2C3C(C=NC3=O)N(C24c5ccc(cc5NC4=O)Cl)CC6CC6
FormulaC23 H18 Cl2 F N3 O2
Name(3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione
ChEMBL
DrugBank
ZINC
PDB chain6i3s Chain A 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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PDB6i3s Targeted Synthesis of Complex Spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-ones by Intramolecular Cyclization of Azomethine Ylides: Highly Potent MDM2-p53 Inhibitors.
Resolution1.77 Å
Binding residue
(original residue number in PDB)		L54 L57 G58 I61 M62 Y67 F86 V93 H96 I99 Y100
Binding residue
(residue number reindexed from 1)		L37 L40 G41 I44 M45 Y50 F69 V76 H79 I82 Y83
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.05,IC50=90nM
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:6i3s, PDBe:6i3s, PDBj:6i3s
PDBsum6i3s
PubMed30458062
UniProtQ00987|MDM2_HUMAN E3 ubiquitin-protein ligase Mdm2 (Gene Name=MDM2)

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