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(-) Description

Title :  CRYSTAL STRUCTURE OF PARP CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS
 
Authors :  Q. F. Liu, T. T. Chen, Y. C. Xu
Date :  10 Oct 12  (Deposition) - 27 Mar 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Keywords :  Polymerase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Ye, C. H. Chen, T. Chen, Z. Song, J. X. He, X. J. Huan, S. S. Song, Q. Liu, Y. Chen, J. Ding, Y. Xu, Z. H. Miao, A. Zhang
Design, Synthesis, And Biological Evaluation Of A Series Of Benzo[De][1, 7]Naphthyridin-7(8H)-Ones Bearing A Functionalized Longer Chain Appendage As Novel Parp1 Inhibitors.
J. Med. Chem. V. 56 2885 2013
PubMed-ID: 23473053  |  Reference-DOI: 10.1021/JM301825T

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 1
    Chains: A, B, C, D
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 660-1101
    Gene: ADPRT, PARP1, PPOL
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   C 
Biological Unit 2 (1x):    D
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):  B  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
115S4Ligand/IonN-{(2S)-1-[4-(4-FLUOROPHENYL)-3,6-DIHYDROPYRIDIN-1(2H)-YL]-1-OXOPROPAN-2-YL}-2-[(9AR)-7-OXO-2,3,7,8,9,9A-HEXAHYDRO-1H-BENZO[DE][1,7]NAPHTHYRIDIN-1-YL]ACETAMIDE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
115S1Ligand/IonN-{(2S)-1-[4-(4-FLUOROPHENYL)-3,6-DIHYDROPYRIDIN-1(2H)-YL]-1-OXOPROPAN-2-YL}-2-[(9AR)-7-OXO-2,3,7,8,9,9A-HEXAHYDRO-1H-BENZO[DE][1,7]NAPHTHYRIDIN-1-YL]ACETAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
115S1Ligand/IonN-{(2S)-1-[4-(4-FLUOROPHENYL)-3,6-DIHYDROPYRIDIN-1(2H)-YL]-1-OXOPROPAN-2-YL}-2-[(9AR)-7-OXO-2,3,7,8,9,9A-HEXAHYDRO-1H-BENZO[DE][1,7]NAPHTHYRIDIN-1-YL]ACETAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
115S1Ligand/IonN-{(2S)-1-[4-(4-FLUOROPHENYL)-3,6-DIHYDROPYRIDIN-1(2H)-YL]-1-OXOPROPAN-2-YL}-2-[(9AR)-7-OXO-2,3,7,8,9,9A-HEXAHYDRO-1H-BENZO[DE][1,7]NAPHTHYRIDIN-1-YL]ACETAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
115S1Ligand/IonN-{(2S)-1-[4-(4-FLUOROPHENYL)-3,6-DIHYDROPYRIDIN-1(2H)-YL]-1-OXOPROPAN-2-YL}-2-[(9AR)-7-OXO-2,3,7,8,9,9A-HEXAHYDRO-1H-BENZO[DE][1,7]NAPHTHYRIDIN-1-YL]ACETAMIDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:49 , ASP A:105 , LEU A:108 , HIS A:201 , GLY A:202 , ARG A:217 , ILE A:218 , ALA A:219 , PRO A:220 , TYR A:228 , PHE A:236 , SER A:243 , TYR A:246BINDING SITE FOR RESIDUE 15S A 401
2AC2SOFTWARELYS A:242 , LEU A:323 , LEU A:324 , TYR A:325BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARELEU B:108 , HIS B:201 , GLY B:202 , ARG B:217 , ILE B:218 , ALA B:219 , PRO B:220 , TYR B:228 , TYR B:235 , PHE B:236 , ALA B:237 , SER B:243 , TYR B:246 , GLU B:327 , HOH B:507BINDING SITE FOR RESIDUE 15S B 401
4AC4SOFTWARELYS B:242 , LEU B:323 , LEU B:324 , TYR B:325BINDING SITE FOR RESIDUE SO4 B 402
5AC5SOFTWARETYR C:49 , ASP C:105 , LEU C:108 , HIS C:201 , GLY C:202 , ARG C:217 , ILE C:218 , ALA C:219 , PRO C:220 , TYR C:228 , GLY C:233 , PHE C:236 , LYS C:242 , SER C:243 , TYR C:246 , GLU C:327BINDING SITE FOR RESIDUE 15S C 401
6AC6SOFTWAREASP D:105 , LEU D:108 , HIS D:201 , GLY D:202 , ARG D:217 , ILE D:218 , ALA D:219 , PRO D:220 , TYR D:228 , TYR D:235 , PHE D:236 , SER D:243 , TYR D:246BINDING SITE FOR RESIDUE 15S D 401
7AC7SOFTWARELYS D:242 , LEU D:324 , TYR D:325BINDING SITE FOR RESIDUE SO4 D 402

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:184 -D:184
2B:184 -C:184

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:63 -Ser A:64
2Gln D:44 -Ile D:45
3Gln D:185 -Arg D:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HHZ)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4hhza1 A:1-135 automated matches                                                                                                      d4hhza2 A:136-349 automated matches                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.hhhhh.eeeeeeeeeeeee.hhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee...eee.hhhheee..eee....eee...........eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hhz A   1 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         


Chain B from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hhzb1 B:1-135 automated matches                                                                                                      d4hhzb2 B:136-350 automated matches                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee.hhhhhhhhhh....eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhhee....ee....eee.......eee.eeee.hhh.eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hhz B   1 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 350
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350


Chain C from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hhzc1 C:1-135 automated matches                                                                                                      d4hhzc2 C:136-350 automated matches                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee...eee.hhhheee..eee....eee...........eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hhz C   1 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 350
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350


Chain D from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4hhzd1 D:2-135 automated matches                                                 d4hhzd2 D:136-349 automated matches                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeee....hhhhhhhhhhhhhh.........eeeeeeeeeee......hhhhh....eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee...eee....eeee..eeee...eee...........eeee.hhh.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hhz D   2 SKLPKPVQDLIKMIFDVESMKKAMVEYEIKLSKRQIQAASNRFYTLIPHDDSVQAKAEMLDNLLDIEVAYSLLRGIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 349
                                    11        21        39        72        82|      104       114    || 133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343      
                                                       30|       48|        82|                     119|                                                                                                                                                                                                                            
                                                        39        72         95                      129
   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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (63, 63)

Asymmetric Unit(hide GO term definitions)

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  4hhz
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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 4l6s 4opx 4oqa 4oqb 4pjt 4r5w 4r6e 4rv6 4und 4uxb 4xhu 4zzz 5a00 5ds3 5ha9 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 4HHZ)