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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIM24 PHD-BROMODOMAIN COMPLEXED WITH N-{6-[3-(BENZYLOXY)PHENOXY]-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL}-3,4-DIMETHOXYBENZENE-1-SULFONAMIDE (7B)
 
Authors :  G. Poncet-Montange, W. Palmer, P. Jones
Date :  18 Feb 15  (Deposition) - 24 Jun 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Center For Biomolecular Structure And Function, Bromodomain, Trim24, Inhibitor, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Palmer, G. Poncet-Montange, G. Liu, A. Petrocchi, N. Reyna, G. Subramanian, J. Theroff, A. Yau, M. Kost-Alimova, J. P. Bardenhagen, E. Leo, H. E. Shepard, T. N. Tieu, X. Shi, Y. Zhan, S. Zhao, M. C. Barton, G. Draetta, C. Toniatti, P. Jones, M. Geck Do, J. N. Andersen
Structure-Guided Design Of Iacs-9571, A Selective High-Affinity Dual Trim24-Brpf1 Bromodomain Inhibitor.
J. Med. Chem. V. 59 1440 2016
PubMed-ID: 26061247  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00405

(-) Compounds

Molecule 1 - TRANSCRIPTION INTERMEDIARY FACTOR 1-ALPHA
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN (UNP RESIDUES 824-1006)
    Gene: TRIM24, RNF82, TIF1, TIF1A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TIF1-ALPHA,E3 UBIQUITIN-PROTEIN LIGASE TRIM24,RING FINGER PROTEIN 82,TRIPARTITE MOTIF-CONTAINING PROTEIN 24

 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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
14BJ2Ligand/IonN-{6-[3-(BENZYLOXY)PHENOXY]-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL}-3,4-DIMETHOXYBENZENESULFONAMIDE
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
14BJ-1Ligand/IonN-{6-[3-(BENZYLOXY)PHENOXY]-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL}-3,4-DIMETHOXYBENZENESULFONAMIDE
2GOL2Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
14BJ2Ligand/IonN-{6-[3-(BENZYLOXY)PHENOXY]-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL}-3,4-DIMETHOXYBENZENESULFONAMIDE
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:829 , CYS A:832 , HIS A:849 , CYS A:852binding site for residue ZN A 1101
02AC2SOFTWARECYS A:841 , CYS A:844 , CYS A:867 , CYS A:870binding site for residue ZN A 1102
03AC3SOFTWAREALA A:977 , GLU A:978 , PHE A:979 , ASN A:980 , GLU A:981 , HOH A:1477binding site for residue GOL A 1103
04AC4SOFTWARETYR A:936 , LYS A:937 , ILE A:938 , ILE A:939 , LYS A:940binding site for residue GOL A 1104
05AC5SOFTWARELEU A:922 , ALA A:923 , PHE A:924 , VAL A:928 , PRO A:929 , PHE A:979 , ASN A:980 , GLU A:985 , HOH A:1325 , HOH A:1338 , TYR B:936 , THR B:947 , ARG B:951 , TYR B:956 , MET B:958 , HOH B:1286 , HOH B:1309 , HOH B:1379binding site for residue 4BJ B 1101
06AC6SOFTWAREPRO A:927 , LEU A:930 , TYR A:936 , LEU B:922 , ALA B:923 , VAL B:928 , PRO B:929 , VAL B:932 , PHE B:979 , ASN B:980 , VAL B:986 , HOH B:1226 , HOH B:1232 , HOH B:1241 , HOH B:1271 , HOH B:1399binding site for residue 4BJ B 1102
07AC7SOFTWAREARG B:970 , GLU B:998 , HOH B:1366binding site for residue SO4 B 1103
08AC8SOFTWARECYS B:829 , CYS B:832 , HIS B:849 , CYS B:852binding site for residue ZN B 1104
09AC9SOFTWARECYS B:841 , CYS B:844 , CYS B:867 , CYS B:870binding site for residue ZN B 1105
10AD1SOFTWAREPRO B:902 , ARG B:906 , HOH B:1234 , HOH B:1343binding site for residue GOL B 1106
11AD2SOFTWAREALA B:977 , GLU B:978 , PHE B:979 , ASN B:980binding site for residue GOL B 1107
12AD3SOFTWAREARG B:871 , ASP B:872 , LEU B:873 , ARG B:910binding site for residue SO4 B 1108

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:854 -Pro A:855
2Val B:854 -Pro B:855

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBM)

(-) 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:177
                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee......ee...............................hhhhh..........hhhhhhhhhhhhhhhhhh..hhhhh........hhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ybm A  824 PNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       883 ||    899       909       919       929       939       949       959       969       979       989       999       
                                                                                       885|                                                                                                                  
                                                                                        892                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee......ee........................................hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ybm B  825 NEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   834       844       854       864       874       884||     906       916       926       936       946       956       966       976       986       996      1006
                                                                                      885|                                                                                                            
                                                                                       898
   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 4YBM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TIF1A_HUMAN | O15164: 2yyn 3o33 3o34 3o35 3o36 3o37 4yab 4yad 4yat 4yax 4ybs 4ybt 4yc9 4zql 5h1t 5h1u 5h1v

(-) Related Entries Specified in the PDB File

4yab 4yad 4yat 4yax 4ybs 4ybt 4yc9