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(-) Description

Title :  MDM2 IN COMPLEX WITH SAR405838
 
Authors :  J. Lmeagher, J. A. Stuckey
Date :  26 Oct 16  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E
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:  A  (2x)
Biol. Unit 7:  B (1x),D (1x)
Biol. Unit 8:  C  (2x)
Keywords :  P53-Binding Protein, Oncoprotein, Double Minute 2 Protein, Small Molecule Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wang, W. Sun, Y. Zhao, D. Mceachern, I. Meaux, C. Barriere, J. A. Stuckey, J. L. Meagher, L. Bai, L. Liu, C. G. Hoffman-Luca, J. Lu, S. Shangary, S. Yu, D. Bernard, A. Aguilar, O. Dos-Santos, L. Besret, S. Guerif, P. Pannier, D. Gorge-Bernat, L. Debussche
Sar405838: An Optimized Inhibitor Of Mdm2-P53 Interaction That Induces Complete And Durable Tumor Regression.
Cancer Res. V. 74 5855 2014
PubMed-ID: 25145672  |  Reference-DOI: 10.1158/0008-5472.CAN-14-0799

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, B, C, D, E
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 10-118
    Gene: MDM2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
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 (2x): A    
Biological Unit 7 (1x):  B (1x) D (1x) 
Biological Unit 8 (2x):   C  

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
17HC5Ligand/Ion(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
2GOL7Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
17HC1Ligand/Ion(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
2GOL3Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
17HC1Ligand/Ion(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
2GOL2Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
17HC1Ligand/Ion(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
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
17HC1Ligand/Ion(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
2GOL-1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
17HC1Ligand/Ion(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
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 6 (3, 10)
No.NameCountTypeFull Name
17HC2Ligand/Ion(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
2GOL6Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 7 (2, 3)
No.NameCountTypeFull Name
17HC1Ligand/Ion(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
2GOL2Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 8 (3, 8)
No.NameCountTypeFull Name
17HC2Ligand/Ion(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
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:10 , VAL A:14 , THR A:16 , LEU A:54 , GLY A:58 , GLN A:59 , ILE A:61 , MET A:62 , TYR A:67 , VAL A:93 , LYS A:94 , HIS A:96 , ILE A:99 , TYR A:100binding site for residue 7HC A 201
02AC2SOFTWARELYS A:45 , ASP A:46 , THR A:47binding site for residue SO4 A 202
03AC3SOFTWARETYR A:104 , VAL A:109 , HOH A:304 , HOH A:310 , HOH A:313 , HOH A:342binding site for residue GOL A 203
04AC4SOFTWAREARG A:105 , HOH A:334 , GLY B:87 , ARG B:105 , ARG C:105 , ARG D:105binding site for residue GOL A 204
05AC5SOFTWAREASP A:84 , LEU A:85 , ARG A:105 , HOH A:309 , HOH C:313 , LYS D:31 , TYR D:104 , ARG D:105 , LEU D:107binding site for residue GOL A 205
06AC6SOFTWAREVAL B:14 , THR B:16 , LEU B:54 , GLY B:58 , ILE B:61 , MET B:62 , TYR B:67 , VAL B:93 , HIS B:96 , ILE B:99 , TYR B:100 , GOL B:203 , THR D:10 , GLN D:59 , MET D:62binding site for residue 7HC B 201
07AC7SOFTWAREALA B:13 , VAL B:14 , THR B:15 , LYS B:51 , HOH B:335 , ALA D:13 , THR D:15 , LYS D:51binding site for residue GOL B 202
08AC8SOFTWAREPHE B:55 , GLY B:58 , GLN B:59 , 7HC B:201 , HOH B:301 , 7HC D:201binding site for residue GOL B 203
09AC9SOFTWAREVAL C:14 , THR C:16 , LEU C:54 , LEU C:57 , GLY C:58 , GLN C:59 , ILE C:61 , TYR C:67 , PHE C:86 , VAL C:93 , LYS C:94 , HIS C:96 , ILE C:99 , TYR C:100binding site for residue 7HC C 201
10AD1SOFTWARELYS C:45 , ASP C:46 , THR C:47binding site for residue SO4 C 202
11AD2SOFTWARELYS C:98 , THR C:101 , HOH C:301 , HOH C:313 , HOH C:321 , HOH C:332binding site for residue GOL C 203
12AD3SOFTWAREILE A:74 , PHE A:91 , SER A:92 , TYR C:76 , SER C:78 , PRO C:89binding site for residue GOL C 204
13AD4SOFTWAREGLN B:59 , GOL B:203 , VAL D:14 , THR D:16 , LEU D:54 , GLY D:58 , ILE D:61 , MET D:62 , VAL D:93 , HIS D:96 , ILE D:99 , TYR D:100binding site for residue 7HC D 201
14AD5SOFTWARETHR E:10 , VAL E:14 , THR E:16 , LEU E:54 , GLY E:58 , ILE E:61 , MET E:62 , TYR E:67 , HIS E:73 , VAL E:93 , HIS E:96 , ILE E:99 , TYR E:100binding site for residue 7HC E 201
15AD6SOFTWARELYS E:45 , ASP E:46 , THR E:47binding site for residue SO4 E 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TRF)

(-) 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:98
                                                                                                                                  
               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
                 5trf A  10 TDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    19        29        39        49        59       |73        83        93       103        
                                                                                    67|                                       
                                                                                     72                                       


Chain B from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh......eee...hhhhhhhh..eee..hhhhhhhhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5trf B  10 TDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQ 112
                                    19        29        39        49        59       |72        82        92       102       112
                                                                                    67|                                         
                                                                                     71                                         


Chain C from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhhh.ee.....eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5trf C  11 DGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    20        30        40        50        60        70        80        90       100       110


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh......eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5trf D  10 TDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    19        29        39        49        59        72        82        92       102        
                                                                                     68|                                      
                                                                                      72                                      


Chain E from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh..ee.....eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5trf E  10 TDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    19        29        39        49        59        69        79        89        99       109
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5TRF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

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  5trf
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  MDM2_HUMAN | Q00987
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  6.3.2.-
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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 5lay 5laz 5ln2 5mnj

(-) Related Entries Specified in the PDB File

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