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(-) Description

Title :  CRYSTAL STRUCTURE-BASED DESIGN AND DISOVERY OF A NOVEL PARP1 ANTIAGONIST (BL-PA10) THAT INDUCES APOPTOSIS AND INHIBITS METASTASIS IN TRIPLE NEGATIVE BREAST CANCER
 
Authors :  L. Fu, H. Peng, L. Zhang, L. Ouyang
Date :  30 Dec 15  (Deposition) - 09 Mar 16  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Fu, S. Wang, X. Wang, P. Wang, Y. Zheng, D. Yao, M. Guo, L. Zhang, L. Ouyang
Crystal Structure-Based Discovery Of A Novel Synthesized Parp1 Inhibitor (Ol-1) With Apoptosis-Inducing Mechanisms I Triple-Negative Breast Cancer
Sci Rep V. 6 3 2016
PubMed-ID: 27920426  |  Reference-DOI: 10.1038/S41598-016-0007-2

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 1
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: UNP RESIDUES 662-1011
    Gene: PARP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARP-1,ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 1,ARTD1, NAD(+) ADP-RIBOSYLTRANSFERASE 1,ADPRT 1,POLY[ADP-RIBOSE] SYNTHASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
3TP01Ligand/IonAMITRIPTYLINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:105 , ARG A:217 , ILE A:218 , ALA A:219 , LYS A:232 , GLY A:233 , TYR A:235binding site for residue GOL A 401
2AC2SOFTWARELYS A:242 , LEU A:323 , LEU A:324 , TYR A:325binding site for residue SO4 A 402
3AC3SOFTWAREPRO A:281 , LYS A:282 , LYS B:284binding site for residue SO4 A 403
4AC4SOFTWAREASP B:105 , ALA B:219 , GLY B:233 , TYR B:235 , TP0 B:406binding site for residue GOL B 401
5AC5SOFTWARELYS B:242 , LEU B:324 , TYR B:325binding site for residue SO4 B 402
6AC6SOFTWAREGLN A:61 , LYS B:42 , ARG B:43 , LYS B:292binding site for residue SO4 B 403
7AC7SOFTWARELYS B:126 , LYS B:155binding site for residue SO4 B 404
8AC8SOFTWAREARG B:197 , MET B:268 , LYS B:288binding site for residue SO4 B 405
9AC9SOFTWAREGLU B:102 , ASP B:109 , HIS B:201 , GLY B:202 , SER B:203 , ILE B:211 , TYR B:235 , SER B:243 , TYR B:246 , GOL B:401binding site for residue TP0 B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HA9)

(-) Exons   (0, 0)

(no "Exon" information available for 5HA9)

(-) Sequences/Alignments

Asymmetric/Biological 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......ee..eeeeeeeee.hhhhhhhhhh....eeeeeeeehhhhhhhhhhh.........hhhhh.....eee..hhhhhhhh........eeeeeeeeee...eeee..............eeee...eee......ee..ee.....eee...........eeee.hhh.eeeeeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ha9 A   0 MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 350
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349 


Chain B from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....ee....hhhhhhhhhhhhhh.......eeeeeeeeee....hhhhhhh.......eeeeee..hhhhhhhhhhhh........hhhhh.....ee...hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee....eeee..eeee...eee.......eee.eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ha9 B   0 MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 350
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349
   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 5HA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HA9)

(-) Gene Ontology  (63, 63)

Asymmetric/Biological Unit(hide GO term definitions)

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  5ha9
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  PARP1_HUMAN | P09874
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  2.4.2.30
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARP1_HUMAN | P09874: 1uk0 1uk1 1wok 2cok 2cr9 2cs2 2dmj 2jvn 2l30 2l31 2n8a 2rcw 2rd6 2riq 3gjw 3gn7 3l3l 3l3m 3od8 3oda 3odc 3ode 4av1 4dqy 4gv7 4hhy 4hhz 4l6s 4opx 4oqa 4oqb 4pjt 4r5w 4r6e 4rv6 4und 4uxb 4xhu 4zzz 5a00 5ds3 5kpn 5kpo 5kpp 5kpq 5wrq 5wry 5wrz 5ws0 5ws1 5wtc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HA9)