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(-) Description

Title :  THE 1.9A CRYSTAL STRUCTURE OF HUMANIZED XENOPUS MDM2 WITH RO5313109 - A PYRROLIDINE MDM2 INHIBITOR
 
Authors :  B. J. Graves, C. A. Janson, C. Lukacs
Date :  21 Mar 13  (Deposition) - 24 Jul 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Inhibitor Complex, Pyrrolidine, E3 Ubiquitin Ligase, P53, Nucleus, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Ding, Z. Zhang, J. J. Liu, N. Jiang, J. Zhang, T. M. Ross, X. J. Chu, D. Bartkovitz, F. Podlaski, C. Janson, C. Tovar, Z. M. Filipovic, B. Higgins, K. Glenn, K. Packman, L. T. Vassilev, B. Graves
Discovery Of Rg7388, A Potent And Selective P53-Mdm2 Inhibitor In Clinical Development.
J. Med. Chem. V. 56 5979 2013
PubMed-ID: 23808545  |  Reference-DOI: 10.1021/JM400487C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUBS 520
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 21-105)
    Gene: MDM2
    Mutation: YES
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: DOUBLE MINUTE 2 PROTEIN, XDM2, P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1I092Ligand/Ion(3R,4R,5S)-3-(3-CHLOROPHENYL)-4-(4-CHLOROPHENYL)-4-CYANO-N-[(3S)-3,4-DIHYDROXYBUTYL]-5-(2,2-DIMETHYLPROPYL)-D-PROLINAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1I091Ligand/Ion(3R,4R,5S)-3-(3-CHLOROPHENYL)-4-(4-CHLOROPHENYL)-4-CYANO-N-[(3S)-3,4-DIHYDROXYBUTYL]-5-(2,2-DIMETHYLPROPYL)-D-PROLINAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1I091Ligand/Ion(3R,4R,5S)-3-(3-CHLOROPHENYL)-4-(4-CHLOROPHENYL)-4-CYANO-N-[(3S)-3,4-DIHYDROXYBUTYL]-5-(2,2-DIMETHYLPROPYL)-D-PROLINAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:50 , ILE A:57 , MET A:58 , HIS A:69 , PHE A:82 , VAL A:89 , LYS A:90 , HIS A:92 , ILE A:95 , TYR A:96 , HOH A:331 , HOH A:332BINDING SITE FOR RESIDUE I09 A 201
2AC2SOFTWARELEU B:50 , GLY B:54 , MET B:58 , HIS B:69 , VAL B:89 , LYS B:90 , HIS B:92 , HOH B:325 , HOH B:326BINDING SITE FOR RESIDUE I09 B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JRG)

(-) 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:84
                                                                                                                    
               SCOP domains d4jrga_ A: MDM2                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eehhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4jrg A  21 EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLV 104
                                    30        40        50        60        70        80        90       100    


Chain B from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains d4jrgb_ B: MDM2                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.......hhhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4jrg B  21 EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLV 104
                                    30        40        50        60        70        80        90       100
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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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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_XENLA | P56273: 1ttv 1ycq 4ipf 4j3e 4j74 4j7d 4j7e 4jsc 4lwt 4lwu 4lwv

(-) Related Entries Specified in the PDB File

4ipf SAME PROTEIN WITH RG7112, A NUTLIN IN CLINICAL DEVELOPMENT