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(-) Description

Title :  DISCOVERY OF NEW NATURAL-PRODUCT-INSPIRED SPIRO-OXINDOLE COMPOUNDS AS ORALLY ACTIVE INHIBITORS OF THE MDM2-P53 INTERACTION: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6G
 
Authors :  D. Kessler, A. Gollner
Date :  15 Jun 16  (Deposition) - 02 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Vienna, Ppi, Mdm2, Hdm2, Bi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gollner, D. Rudolph, H. Arnhof, M. Bauer, S. M. Blake, G. Boehmelt, X. L. Cockroft, G. Dahmann, P. Ettmayer, T. Gerstberger, J. Karolyi-Oezguer, D. Kessler, C. Kofink, J. Ramharter, J. Rinnenthal, A. Savchenko, R. Schnitzer, H. Weinstabl, U. Weyer-Czernilofsky, T. Wunberg, D. B. Mcconnell
Discovery Of Novel Spiro[3H-Indole-3, 2'-Pyrrolidin]-2(1H)-One Compounds As Chemically Stable And Orally Active Inhibitors Of The Mdm2-P53 Interaction.
J. Med. Chem. V. 59 10147 2016
PubMed-ID: 27775892  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00900

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, B, C, D, E, F
    EC Number: 6.3.2.-
    Fragment: TRUNCATED N-TERMINAL DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: EXTERNAL
    Synonym: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
16SS6Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL5Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
16SS1Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL3Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
16SS1Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
16SS1Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
16SS1Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 5 (3, 3)
No.NameCountTypeFull Name
16SS1Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
16SS1Ligand/Ion(3~{S},3'~{S},4'~{S},5'~{S})-4'-AZANYL-6-CHLORANYL-3'-(3-CHLORANYL-2-FLUORANYL-PHENYL)-1'-[(3-ETHOXYPHENYL)METHYL]-5'-METHYL-SPIRO[1~{H}-INDOLE-3,2'-PYRROLIDINE]-2-ONE
2GOL-1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:71 , GLN A:72 , HIS A:73binding site for residue GOL A 201
02AC2SOFTWAREPRO A:20 , ALA A:21 , SER A:22 , LYS A:36binding site for residue GOL A 202
03AC3SOFTWARELYS A:45 , GLU A:52 , HOH A:316 , THR B:26 , TYR B:104binding site for residue GOL A 203
04AC4SOFTWARESER A:17 , GLN A:18 , ILE A:19 , GLN A:24 , HIS A:96binding site for residue SO4 A 204
05AC5SOFTWARELEU A:54 , GLY A:58 , ILE A:61 , TYR A:67 , GLN A:72 , PHE A:86 , VAL A:93 , HIS A:96 , ILE A:99 , HOH A:302 , GLU C:69 , GLN C:72binding site for residue 6SS A 205
06AC6SOFTWAREASP B:46 , THR B:47binding site for residue SO4 B 201
07AC7SOFTWARELEU B:54 , GLY B:58 , ILE B:61 , MET B:62 , TYR B:67 , GLN B:72 , PHE B:86 , VAL B:93 , HIS B:96 , ILE B:99binding site for residue 6SS B 202
08AC8SOFTWAREGLN C:18 , ILE C:19 , GLN C:24 , HIS C:96 , 6SS C:202binding site for residue GOL C 201
09AC9SOFTWARELEU C:54 , GLY C:58 , ILE C:61 , MET C:62 , TYR C:67 , GLN C:72 , PHE C:86 , VAL C:93 , HIS C:96 , ILE C:99 , GOL C:201 , HOH C:307binding site for residue 6SS C 202
10AD1SOFTWARESER D:17 , GLN D:18 , ILE D:19 , GLN D:24 , HIS D:96binding site for residue SO4 D 201
11AD2SOFTWARELEU D:54 , GLY D:58 , ILE D:61 , MET D:62 , TYR D:67 , GLN D:72 , PHE D:86 , VAL D:93 , HIS D:96 , ILE D:99 , HOH D:305binding site for residue 6SS D 202
12AD3SOFTWARE6SS E:203binding site for residue GOL E 201
13AD4SOFTWARELYS E:45 , ASP E:46 , THR E:47binding site for residue SO4 E 202
14AD5SOFTWARELEU E:54 , GLY E:58 , ILE E:61 , TYR E:67 , PHE E:86 , VAL E:93 , HIS E:96 , ILE E:99 , GOL E:201binding site for residue 6SS E 203
15AD6SOFTWARELEU F:54 , GLY F:58 , ILE F:61 , MET F:62 , TYR F:67 , HIS F:96 , ILE F:99binding site for residue 6SS F 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LAY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LAY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LAY)

(-) Exons   (0, 0)

(no "Exon" information available for 5LAY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhhhhhhhh......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5lay A  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    26        36        46        56        66        76        86        96       106     


Chain B from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhheeeehhhhhhhhhhh......eehhhhhhhhhhhhhhh..ee..eeeeee...hhhhhhhh..eee..hhhhhhhhhhhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5lay B  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    27        37        47        57        67        77        87        97       107    


Chain C from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5lay C  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    27        37        47        57        67        77        87        97       107    


Chain D from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhee..hhhhhhhhhh.......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5lay D  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    26        36        46        56        66        76        86        96       106    


Chain E from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhheeeehhhhhhhhhh.......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5lay E  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    27        37        47        57        67        77        87        97       107    


Chain F from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhhhhhhh.......eehhhhhhhhhhhhhhhh.........ee...hhhhhhhh..ee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 5lay F  23 EQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSEHRKIYTMIYR 105
                                    32        42        52        62        72        82        92|      104 
                                                                                                92|          
                                                                                                 95
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LAY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LAY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LAY)

(-) Gene Ontology  (83, 83)

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  5lay
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MDM2_HUMAN | Q00987: 1rv1 1t4e 1t4f 1ycr 1z1m 2axi 2c6a 2c6b 2f1y 2fop 2gv2 2hdp 2lzg 2m86 2mps 2ruh 2vje 2vjf 3eqs 3g03 3iux 3iwy 3jzk 3jzr 3jzs 3lbk 3lbl 3lnj 3lnz 3mqs 3tj2 3tpx 3tu1 3v3b 3vbg 3vzv 3w69 4dij 4ere 4erf 4hbm 4hfz 4hg7 4jv7 4jv9 4jve 4jvr 4jwr 4mdn 4mdq 4oas 4oba 4occ 4ode 4odf 4ogn 4ogt 4ogv 4oq3 4qo4 4qoc 4ud7 4ue1 4umn 4wt2 4xxb 4zfi 4zgk 4zyc 4zyf 4zyi 5afg 5c5a 5hmh 5hmi 5hmk 5j7f 5j7g 5lav 5law 5laz 5ln2 5mnj 5trf

(-) Related Entries Specified in the PDB File

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