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(-) Description

Title :  HDM2 IN COMPLEX WITH A 3,3-DISUBSTITUTED PIPERIDINE
 
Authors :  G. Scapin
Date :  16 Jan 16  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Oncology, E3 Ubiquitin-Protein Ligase, P53/Tp53, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. L. Bogen, W. Pan, C. R. Gibeau, B. R. Lahue, Y. Ma, L. G. Nair, E. Seigel G. W. Shipps, Y. Tian, Y. Wang, Y. Lin, M. Liu, S. Liu, A. Mirza, X. Wang, P. Lipari, C. Seidel-Dugan, D. J. Hicklin, W. R. Bishop, D. Rindgen, A. Nomeir, W. Prosise, P. Reichert, G. Scapin, C. Strickland, R. J. Dol
Discovery Of Novel 3, 3-Disubstituted Piperidines As Orally Bioavailable, Potent, And Efficacious Hdm2-P53 Inhibitors.
Acs Med. Chem. Lett. V. 7 324 2016
PubMed-ID: 26985323  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00472

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MDM2
    Mutation: YES
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
162T2Ligand/Ion{4-[2-(2-HYDROXYETHOXY)PHENYL]PIPERAZIN-1-YL}[(2R,3S)-2-PROPYL-1-{[4-(TRIFLUOROMETHYL)PYRIDIN-3-YL]CARBONYL}-3-{[5-(TRIFLUOROMETHYL)THIOPHEN-3-YL]OXY}PIPERIDIN-3-YL]METHANONE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
162T1Ligand/Ion{4-[2-(2-HYDROXYETHOXY)PHENYL]PIPERAZIN-1-YL}[(2R,3S)-2-PROPYL-1-{[4-(TRIFLUOROMETHYL)PYRIDIN-3-YL]CARBONYL}-3-{[5-(TRIFLUOROMETHYL)THIOPHEN-3-YL]OXY}PIPERIDIN-3-YL]METHANONE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
162T1Ligand/Ion{4-[2-(2-HYDROXYETHOXY)PHENYL]PIPERAZIN-1-YL}[(2R,3S)-2-PROPYL-1-{[4-(TRIFLUOROMETHYL)PYRIDIN-3-YL]CARBONYL}-3-{[5-(TRIFLUOROMETHYL)THIOPHEN-3-YL]OXY}PIPERIDIN-3-YL]METHANONE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
162T2Ligand/Ion{4-[2-(2-HYDROXYETHOXY)PHENYL]PIPERAZIN-1-YL}[(2R,3S)-2-PROPYL-1-{[4-(TRIFLUOROMETHYL)PYRIDIN-3-YL]CARBONYL}-3-{[5-(TRIFLUOROMETHYL)THIOPHEN-3-YL]OXY}PIPERIDIN-3-YL]METHANONE
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:24 , LEU A:54 , GLY A:58 , ILE A:61 , MET A:62 , TYR A:67 , GLN A:72 , PHE A:91 , VAL A:93 , HIS A:96 , ILE A:99 , TYR A:100 , HOH A:1136 , HOH A:1137 , LYS B:51 , TYR B:55 , 62T B:1001 , HOH B:1115binding site for residue 62T A 1001
2AC2SOFTWAREGLU A:95 , HIS A:96 , ARG A:97binding site for residue SO4 A 1002
3AC3SOFTWARELYS A:51 , 62T A:1001 , LEU B:54 , GLY B:58 , ILE B:61 , TYR B:67 , GLN B:72 , PHE B:91 , VAL B:93 , HIS B:96 , ILE B:99 , TYR B:100 , HOH B:1102 , HOH B:1108 , HOH B:1115 , HOH B:1125binding site for residue 62T B 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:21 -Ser A:22
2Ala B:21 -Ser B:22
3Gln B:113 -Glu B:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HMI)

(-) 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:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 5hmi A  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLYYLGQYIMTKRLYDEKQQHIVHCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQ 113
                                    27        37        47        57        67        77        87        97       107      


Chain B from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5hmi B  20 PASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLYYLGQYIMTKRLYDEKQQHIVHCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSAGA 119
                                    29        39        49        59        69        79        89        99       109       119
   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  (0, 0)

(no "SCOP Domain" information available for 5HMI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5hmi
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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 5hmk 5j7f 5j7g 5lav 5law 5lay 5laz 5ln2 5mnj 5trf

(-) Related Entries Specified in the PDB File

5hmh 5hmk