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(-) Description

Title :  STRUCTURE OF PARP2 CATALYTIC DOMAIN BOUND TO AN ISOINDOLINONE INHIBITOR
 
Authors :  E. Casale, M. Fasolini, G. Papeo, H. Posteri, D. Borghi, A. A. Busel, F. C M. Ciomei, A. Cirla, E. Corti, M. Danello, M. Fasolini, E. R. Felder, B. A. Galvani, A. Isacchi, A. Khvat, M. Y. Krasavin, R. Lupi, P. Orsini, R. E. Pesenti, D. Pezzetta, S. Rainoldi, F. Riccardisirtori, A. Scolaro F. Zuccotto, D. Donati, A. Montagnoli
Date :  15 Apr 15  (Deposition) - 12 Aug 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. E. Papeo, H. Posteri, D. Borghi, A. A. Busel, F. Caprera, E. Casale M. Ciomei, A. Cirla, E. Corti, M. D'Anello, M. Fasolini, B. Forte, A. Galvani, A. Isacchi, A. Khvat, M. Y. Krasavin, R. Lupi, P. Orsini, R. Perego, E. Pesenti, D. Pezzetta, S. Rainoldi, F. Riccardi-Sirtori A. Scolaro, F. Sola, F. Zuccotto, E. R. Felder, D. Donati, A. Montagnol
Discovery Of 2-[1-(4, 4-Difluorocyclohexyl)Piperidin-4-Yl]-6- Fluoro-3-Oxo-2, 3-Dihydro-1H-Isoindole-4-Carboxamide (Nms- P118): A Potent, Orally Available And Highly Selective Parp- 1 Inhibitor For Cancer Therapy.
J. Med. Chem. V. 58 6875 2015
PubMed-ID: 26222319  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00680

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 2
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 223-583
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARP-2, HPARP-2, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 2, ARTD2, NAD(+) ADP-RIBOSYLTRANSFERASE 2, ADPRT-2, POLYADP-RIBOSE SYNTHASE 2, PADPRT-2, PARP-2, HPARP-2, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 2, ARTD2, NAD(+) ADP-RIBOSYLTRANSFERASE 2, A DPRT-2, POLYADP-RIBOSE SYNTHASE 2, PADPRT-2, POLY ADP-RIBOSE POLYMERASE 2, POLY ADP-RIBOSE POLYMERASE 2

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FSU2Ligand/Ion2-(3-METHOXYPROPYL)-3-OXO-2,3-DIHYDRO-1H-ISOINDOLE-4-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FSU1Ligand/Ion2-(3-METHOXYPROPYL)-3-OXO-2,3-DIHYDRO-1H-ISOINDOLE-4-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FSU1Ligand/Ion2-(3-METHOXYPROPYL)-3-OXO-2,3-DIHYDRO-1H-ISOINDOLE-4-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:328 , HIS A:428 , GLY A:429 , GLY A:454 , TYR A:462 , PHE A:463 , SER A:470 , TYR A:473 , HOH A:2162 , HOH A:2163BINDING SITE FOR RESIDUE FSU A1584
2AC2SOFTWARESER B:328 , ILE B:331 , HIS B:428 , GLY B:429 , GLY B:454 , TYR B:462 , PHE B:463 , SER B:470 , TYR B:473 , HOH B:2149BINDING SITE FOR RESIDUE FSU B1584

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:539 -Pro A:540
2Gly B:539 -Pro B:540

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZZX)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhheeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh........hhhhh.....eee..hhhhhhhhhh......eeeeeeeeee...eeee.....hhhhhh....eeee.eeeee.hhhheee..eee....eee........eee.eeee.hhh.eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zzx A 231 ESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW 583
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       552       562       572       582 
                                                                                                                                                                                                                                                                                                                                                       548|                                
                                                                                                                                                                                                                                                                                                                                                        551                                


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh........hhhhh.....eee..hhhhhhhhhh......eeeeeeeeee...eeee.....hhhhhh....eeee.eeeee.hhhheee..eee....eee..........eee.eeee.hhh.eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zzx B 233 QLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW 583
                                   242       252       262       272       282       292       302       312       322       332       342       352||     364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574         
                                                                                                                                                  353|                                                                                                                                                                                                                                   
                                                                                                                                                   356
   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 4ZZX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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  4zzx
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  PARP2_HUMAN | Q9UGN5
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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
        PARP2_HUMAN | Q9UGN5: 3kcz 3kjd 4pjv 4tvj 4zzy 5d5k 5dsy

(-) Related Entries Specified in the PDB File

4zzy STRUCTURE OF HUMAN PARP2 CATALYTIC DOMAIN BOUND TO AN ISOINDOLINONE INHIBITOR
4zzz STRUCTURE OF HUMAN PARP1 CATALYTIC DOMAIN BOUND TO AN ISOINDOLINONE INHIBITOR
5a00 STRUCTURE OF HUMAN PARP1 CATALYTIC DOMAIN BOUND TO AN ISOINDOLINONE INHIBITOR