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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPOUND 16 BOUND TO MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
 
Authors :  X. Huang
Date :  19 Jun 14  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,C,E,G,I,K
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  G  (1x)
Biol. Unit 5:  I  (1x)
Biol. Unit 6:  K  (1x)
Keywords :  Mdm2, P53, Protein-Protein Interaction, Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, J. Zhu, J. J. Liu, X. Chen, J. Mihalic, J. Deignan, M. Yu, D. Sun, F. Kayser, L. R. Mcgee, M. C. Lo, A. Chen, J. Zhou, Q. Ye, X. Huang, A. M. Long, P. Yakowec, J. D. Oliner, S. H. Olson, J. C. Medina
Optimization Beyond Amg 232: Discovery And Sar Of Sulfonamides On A Piperidinone Scaffold As Potent Inhibitor Of The Mdm2-P53 Protein-Protein Interaction.
Bioorg. Med. Chem. Lett. V. 24 3782 2014
PubMed-ID: 25042256  |  Reference-DOI: 10.1016/J.BMCL.2014.06.073

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, C, E, G, I, K
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

  123456
Asymmetric Unit : ACEGIK
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  C    
Biological Unit 3 (1x):   E   
Biological Unit 4 (1x):    G  
Biological Unit 5 (1x):     I 
Biological Unit 6 (1x):      K

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
135T6Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
135T1Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
135T1Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
135T1Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
135T1Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
135T1Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
135T1Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:54 , GLY A:58 , ILE A:61 , MET A:62 , TYR A:67 , VAL A:93 , LYS A:94 , HIS A:96 , ILE A:99 , TYR A:100 , HOH A:306 , HOH A:324 , HOH A:337 , HOH A:344 , HOH A:357 , GLN K:18 , ARG K:97 , LYS K:98BINDING SITE FOR RESIDUE 35T A 201
2AC2SOFTWARELEU C:54 , GLY C:58 , ILE C:61 , TYR C:67 , VAL C:93 , LYS C:94 , HIS C:96 , ILE C:99 , TYR C:100 , HOH C:314 , HOH C:324 , HOH C:391 , ARG G:97 , LYS G:98BINDING SITE FOR RESIDUE 35T C 201
3AC3SOFTWAREARG C:97 , LYS C:98 , THR C:101 , LEU E:54 , LEU E:57 , GLY E:58 , GLN E:59 , ILE E:61 , TYR E:67 , VAL E:93 , LYS E:94 , HIS E:96 , ILE E:99 , TYR E:100 , HOH E:311 , HOH E:342BINDING SITE FOR RESIDUE 35T E 201
4AC4SOFTWAREGLY G:58 , ILE G:61 , TYR G:67 , VAL G:93 , LYS G:94 , HIS G:96 , ILE G:99 , HOH G:312 , HOH G:379 , HOH G:387BINDING SITE FOR RESIDUE 35T G 201
5AC5SOFTWAREARG A:97 , LYS A:98 , THR A:101 , LEU I:54 , GLY I:58 , ILE I:61 , TYR I:67 , VAL I:93 , LYS I:94 , HIS I:96 , ILE I:99 , HOH I:302 , HOH I:373BINDING SITE FOR RESIDUE 35T I 201
6AC6SOFTWARELEU K:54 , PHE K:55 , GLY K:58 , GLN K:59 , ILE K:61 , PHE K:86 , VAL K:93 , LYS K:94 , HIS K:96 , ILE K:99 , TYR K:100 , HOH K:332 , HOH K:363BINDING SITE FOR RESIDUE 35T K 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QOC)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeehhhhhhhhh........eehhhhhhhhhhhhhhh...hhhhh.eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4qoc A  19 IPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    28        38        48        58        68        78        88        98       108  


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- 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
                 4qoc C  19 IPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    28        38        48        58        68        78        88        98       108  


Chain E from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 4qoc E  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    26        36        46        56       |67        77        87        97       107    
                                                                          64|                                             
                                                                           66                                             


Chain G from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- 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
                 4qoc G  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    27        37        47        57        67        77        87        97       107    


Chain I from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 4qoc I  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    26        36        46        56        66        76        86        96       106    


Chain K from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4qoc K  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    26        36        46        56        66        76        86        96       106
   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  (0, 0)

(no "SCOP Domain" information available for 4QOC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

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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 4oas 4oba 4occ 4ode 4odf 4ogn 4ogt 4ogv 4oq3 4qo4 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

4qo4