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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF MDM2 WITH INHIBITOR (2'S,3R,4'S,5'R)-N-(2-AMINOETHYL)-6-CHLORO-4'-(3-CHLORO-2-FLUOROPHENYL)-2'-(2,2-DIMETHYLPROPYL)-2-OXO-1,2-DIHYDROSPIRO[INDOLE-3,3'-PYRROLIDINE]-5'-CARBOXAMIDE
 
Authors :  X. Huang, F. Gonzalez-Lopez De Turiso, D. Sun, R. Yosup, M. D. Bartber H. P. Beck, J. Cannon, P. Shaffer, J. D. Oliner, S. H. Olson, J. C. Medina
Date :  26 Mar 13  (Deposition) - 01 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,C,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Keywords :  P53, Protein-Protein Interaction, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Gonzalez-Lopez De Turiso, D. Sun, Y. Rew, M. D. Bartberger, H. P. Beck, J. Canon, A. Chen, D. Chow, T. L. Correll, X. Huang, L. D. Julian, F. Kayser, M. C. Lo, A. M. Long, D. Mcminn, J. D. Oliner, T. Osgood, J. P. Powers, A. Y. Saiki, S. Schneider, P. Shaffer, S. H. Xiao, P. Yakowec, X. Yan, Q. Ye, D. Yu, X. Zhao, J. Zhou, J. C. Medina S. H. Olson
Rational Design And Binding Mode Duality Of Mdm2-P53 Inhibitors.
J. Med. Chem. V. 56 4053 2013
PubMed-ID: 23597064  |  Reference-DOI: 10.1021/JM400293Z

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, C, E
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 18-111
    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

  123
Asymmetric Unit : ACE
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  C 
Biological Unit 3 (1x):   E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
11MT3Ligand/Ion(2'S,3R,4'S,5'R)-N-(2-AMINOETHYL)-6-CHLORO-4'-(3-CHLORO-2-FLUOROPHENYL)-2'-(2,2-DIMETHYLPROPYL)-2-OXO-1,2-DIHYDROSPIRO[INDOLE-3,3'-PYRROLIDINE]-5'-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11MT1Ligand/Ion(2'S,3R,4'S,5'R)-N-(2-AMINOETHYL)-6-CHLORO-4'-(3-CHLORO-2-FLUOROPHENYL)-2'-(2,2-DIMETHYLPROPYL)-2-OXO-1,2-DIHYDROSPIRO[INDOLE-3,3'-PYRROLIDINE]-5'-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11MT1Ligand/Ion(2'S,3R,4'S,5'R)-N-(2-AMINOETHYL)-6-CHLORO-4'-(3-CHLORO-2-FLUOROPHENYL)-2'-(2,2-DIMETHYLPROPYL)-2-OXO-1,2-DIHYDROSPIRO[INDOLE-3,3'-PYRROLIDINE]-5'-CARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11MT1Ligand/Ion(2'S,3R,4'S,5'R)-N-(2-AMINOETHYL)-6-CHLORO-4'-(3-CHLORO-2-FLUOROPHENYL)-2'-(2,2-DIMETHYLPROPYL)-2-OXO-1,2-DIHYDROSPIRO[INDOLE-3,3'-PYRROLIDINE]-5'-CARBOXAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:54 , LEU A:57 , GLY A:58 , MET A:62 , TYR A:67 , HIS A:96 , ILE A:99 , TYR A:100 , HOH A:321 , HOH A:342BINDING SITE FOR RESIDUE 1MT A 201
2AC2SOFTWARELEU C:54 , LEU C:57 , ILE C:61 , MET C:62 , TYR C:67 , VAL C:93 , HIS C:96 , ILE C:99 , TYR C:100BINDING SITE FOR RESIDUE 1MT C 201
3AC3SOFTWARELEU E:54 , GLY E:58 , ILE E:61 , MET E:62 , PHE E:86 , HIS E:96 , ILE E:99 , TYR E:100 , HOH E:302 , HOH E:379 , HOH E:380BINDING SITE FOR RESIDUE 1MT E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JVR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JVR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JVR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JVR)

(-) Exons   (0, 0)

(no "Exon" information available for 4JVR)

(-) 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:89
                                                                                                                         
               SCOP domains d4jvra_ A: MDM2                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhh........eehhhhhhhhhhhhhh......eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4jvr A  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    27        37        47        57        67||      81        91       101         
                                                                             68|                                     
                                                                              73                                     


Chain C from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains d4jvrc_ C: MDM2                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhhhhh.....eehhhhhhhhhhhhhhh.....eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4jvr C  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    27        37        47        57        67||      81        91       101         
                                                                             68|                                     
                                                                              73                                     


Chain E from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains d4jvre_ E: MDM2                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeehhhhhhhhhhhh....eehhhhhhhhhhhhhhh......eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4jvr E  19 IPASEQETLVRPKPLLLKLLKSVGQKDTYTMKEVLFYLGQYIMTKRLYDQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    28        38   ||   49        59        72        82        92       102        
                                                  42|                      68|                                      
                                                   44                       72
   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  (1, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JVR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JVR)

(-) Gene Ontology  (83, 83)

Asymmetric Unit(hide GO term definitions)

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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 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 5trf

(-) Related Entries Specified in the PDB File

4jv7 4jv9 4jve 4jwr