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(-) Description

Title :  STRUCTURE OF A NOVEL SUBMICROMOLAR MDM2 INHIBITOR
 
Authors :  M. Bista, G. Popowicz, T. A. Holak
Date :  23 Aug 13  (Deposition) - 13 Nov 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A
Keywords :  Mdm2, P53, Cancer, Small Molecule, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bista, S. Wolf, K. Khoury, K. Kowalska, Y. Huang, E. Wrona, M. Arciniega, G. M. Popowicz, T. A. Holak, A. Domling
Transient Protein States In Designing Inhibitors Of The Mdm2-P53 Interaction.
Structure V. 21 2143 2013
PubMed-ID: 24207125  |  Reference-DOI: 10.1016/J.STR.2013.09.006

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 18-110
    GeneMDM2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOUBLE MINUTE 2 PROTEIN, HDM2, ONCOPROTEIN MDM2, P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2Y301Ligand/Ion3-{(1S)-2-(TERT-BUTYLAMINO)-1-[{4-[(4-CHLOROBENZYL)OXY]BENZYL}(FORMYL)AMINO]-2-OXOETHYL}-6-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:23 , LYS A:51 , LEU A:54 , PHE A:55 , GLY A:58 , ILE A:61 , MET A:62 , VAL A:93 , HIS A:96 , TYR A:100 , HOH A:328 , HOH A:349 , HOH A:356BINDING SITE FOR RESIDUE Y30 A 201
2AC2SOFTWAREMET A:17 , GLN A:18 , HIS A:96 , HOH A:342BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREARG A:97 , HOH A:327BINDING SITE FOR RESIDUE SO4 A 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MDN)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains d4mdna_ A: MDM2                                                                                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
                 4mdn A  17 MQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    26        36        46        56        66        76        86        96       106    

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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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

Asymmetric/Biological 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 | Q009871rv1 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 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

4mdq