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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF MDM2 (17-111) IN COMPLEX WITH COMPOUND 25
 
Authors :  X. Huang
Date :  06 Jan 14  (Deposition) - 19 Feb 14  (Release) - 12 Mar 14  (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 :  Mdm2. 53, Protein-Protein Interaction, Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Sun, Z. Li, Y. Rew, M. Gribble, M. D. Bartberger, H. P. Beck, J. Canon, A. Chen, X. Chen, D. Chow, J. Deignan, J. Duquette, J. Eksterowicz, B. Fisher, B. M. Fox, J. Fu, A. Z. Gonzalez, F. Gonzalez-Lopez De Turiso, J. B. Houze, X. Huang, M. Jiang, L. Jin, F. Kayser, J. J. Liu, M. C. Lo, A. M. Long, B. Lucas, L. R. Mcgee, J. Mcintosh, J. Mihalic, J. D. Oliner, T. Osgood, M. L. Peterson, P. Roveto, A. Y. Saiki, P. Shaffer, M. Toteva, Y. Wang, Y. C. Wang, S. Wortman, P. Yakowec, X. Yan, Q. Ye, D. Yu, M. Yu, X. Zhao, J. Zhou, J. Zhu, S. H. Olson, J. C. Medina
Discovery Of Amg 232, A Potent, Selective, And Orally Bioavailable Mdm2-P53 Inhibitor In Clinical Development.
J. Med. Chem. V. 57 1454 2014
PubMed-ID: 24456472  |  Reference-DOI: 10.1021/JM401753E

(-) 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 17-111
    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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
12SW3Ligand/Ion[(3R,5R,6S)-1-[(2S)-1-(TERT-BUTYLSULFONYL)BUTAN-2-YL]-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-3-METHYL-2-OXOPIPERIDIN-3-YL]ACETIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12SW1Ligand/Ion[(3R,5R,6S)-1-[(2S)-1-(TERT-BUTYLSULFONYL)BUTAN-2-YL]-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-3-METHYL-2-OXOPIPERIDIN-3-YL]ACETIC ACID
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12SW1Ligand/Ion[(3R,5R,6S)-1-[(2S)-1-(TERT-BUTYLSULFONYL)BUTAN-2-YL]-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-3-METHYL-2-OXOPIPERIDIN-3-YL]ACETIC ACID
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
12SW1Ligand/Ion[(3R,5R,6S)-1-[(2S)-1-(TERT-BUTYLSULFONYL)BUTAN-2-YL]-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-3-METHYL-2-OXOPIPERIDIN-3-YL]ACETIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:54 , GLY A:58 , GLN A:59 , ILE A:61 , VAL A:93 , LYS A:94 , HIS A:96 , ILE A:99 , TYR A:100 , HOH A:321 , ARG E:97BINDING SITE FOR RESIDUE 2SW A 201
2AC2SOFTWAREARG A:97 , LEU C:54 , GLY C:58 , GLN C:59 , ILE C:61 , VAL C:93 , LYS C:94 , HIS C:96 , ILE C:99 , HOH C:340 , HOH C:414BINDING SITE FOR RESIDUE 2SW C 201
3AC3SOFTWAREHOH C:377 , LEU E:54 , GLN E:59 , ILE E:61 , MET E:62 , VAL E:93 , LYS E:94 , HIS E:96 , TYR E:100BINDING SITE FOR RESIDUE 2SW E 201
4AC4SOFTWAREPRO A:20 , ALA A:21 , LYS C:51 , LYS E:51 , HOH E:317 , HOH E:321 , HOH E:342BINDING SITE FOR RESIDUE SO4 E 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OAS)

(-) 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:93
                                                                                                                             
               SCOP domains d4oasa_ A: MDM2                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhh........eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4oas A  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    27        37        47        57        67        77        87        97       107   


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains d4oasc_ C: MDM2                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh...hhhhh.eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4oas C  19 IPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    28        38        48        58        68        78        88        98       108  


Chain E from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains d4oase_ E: MDM2                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhhheee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4oas E  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    27        37        47        57        67        77        87        97       107
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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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 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

4ere 4erf