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(-) Description

Title :  CEREBLON IN COMPLEX WITH DDB1 AND CC-220
 
Authors :  M. Matyskiela, B. Pagarigan, P. Chamberlain
Date :  07 Mar 17  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,C
Keywords :  E3, Ubiquitin Ligase, Crl4, Dcaf, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Matyskiela, W. Zhang, H. W. Man, G. Muller, G. Khambatta, F. Baculi, M. Hickman, L. Lebrun, B. Pagarigan, G. Carmel, C. C. Lu, G. Lu, M. Riley, Y. Satoh, P. Schafer, T. O. Daniel, J. Carmichael, B. E. Cathers, P. P. Chamberlain
A Cereblon Modulator (Cc-220) With Improved Degradation Of Ikaros And Aiolos.
J. Med. Chem. 2017
PubMed-ID: 28425720  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01921

(-) Compounds

Molecule 1 - DNA DAMAGE-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    GeneDDB1, XAP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDDB P127 SUBUNIT,DNA DAMAGE-BINDING PROTEIN A,DDBA,DAMAGE- SPECIFIC DNA-BINDING PROTEIN 1,HBV X-ASSOCIATED PROTEIN 1,XAP-1,UV- DAMAGED DNA-BINDING FACTOR,UV-DAMAGED DNA-BINDING PROTEIN 1,UV-DDB 1, XPE-BINDING FACTOR,XPE-BF,XERODERMA PIGMENTOSUM GROUP E-COMPLEMENTING PROTEIN,XPCE
 
Molecule 2 - PROTEIN CEREBLON
    ChainsC
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    FragmentRESIDUES 40-442
    GeneCRBN, AD-006
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
18W71Ligand/Ion(3S)-3-[4-({4-[(MORPHOLIN-4-YL)METHYL]PHENYL}METHOXY)-1-OXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]PIPERIDINE-2,6-DIONE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:351 , PRO C:352 , GLU C:377 , HIS C:378 , SER C:379 , TRP C:380 , TRP C:386 , TRP C:400 , PHE C:402binding site for residue 8W7 C 501
2AC2SOFTWARECYS C:323 , CYS C:326 , CYS C:391 , CYS C:394binding site for residue ZN C 502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:18 -A:313

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:357 -Pro A:358
2Ser C:410 -Pro C:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V3O)

(-) Exons   (0, 0)

(no "Exon" information available for 5V3O)

(-) 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:1087
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eeeee........eeeeee..eeeeeee....eeeeeeee....eeeeeee........eeeeee...eeeeeeeeee..eeeeeeeeeee.............eeee.....eeeee......eeee...................eeeeee.......eeeeeee....eeeeeeeee....eeeeeeee........eeee.......eeee....eeee....eeee.........eeeeee......eeeeee...eeeeeeee....eeeeeeeee...eeeeee....eeeeee....eeeeee..........eeeeeee.....eeeeeee........eeeeee......eeeeeeee..eeeeeeee.....eeeee..........eeeeee..eeeeeeee..eeeee..........eeeeeee...eeeeee...eeeee.....eeeee................ee.......eeeeeee..eeeeeeee.....eeeee.........eeeee....eeeee........eeee......eeeeeee......eeeeee...eeeeee........eeeeeee......eeeeee....eeeeee....eeeeee..eee..........eeeee.......eeeee...eeeeeee....eeeeeeee...eeeeeeee....eeeeeeeeeee...ee...hhhhh....ee.....eeeeeeeeeee.....eeeeee....eeeeeeeee........eeeeeeee..........eeeeeeee....eeeee..ee......eeee..eeeeee..eeeeeee.....eeeeeeee......eeeee..eeeee.....eeeeee......eeeeeee.....eeeeee....eeeeee...eeeeee........eeeeeee....eeeeee......eeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhh..........eeehhhhhhhhhhhhhhhhhhh...ee...ee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5v3o A    2 SYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQNVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTTALRPSASTQALSSSVSSSKEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDEERQHLQEVGLFHLGEFVNVFCHGSLVMTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDKREATADDLIKVVEELTRIH 1140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       212       222       232       242       252       262       272       282    || 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     ||554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744|      758       768||     792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       988       998      1008     |1027      1037      1047      1057      1067      1077||    1089      1099      1109      1123      1133       
                                                                                                                                                                                                                                         209|                                                                         287|                                                                                                                                                                                                                                                       546|                                                                                                                                                                                              744|                 769|                                                                                                                                                                                                 980|                       1014|                                                  1078|                               1116|                   
                                                                                                                                                                                                                                          211                                                                          296                                                                                                                                                                                                                                                        551                                                                                                                                                                                               749                  784                                                                                                                                                                                                  987                        1024                                                   1081                                1121                   

Chain C from PDB  Type:PROTEIN  Length:363
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...ee...........eeeee.............eeeeee.hhhhhhhhhhhhhh..eeeeee....eeeeeeeeeeeeehhhhh.eeeeeeeeeeeeeeeeeee.....eeeeeee.................hhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee......eeee.hhh........eeeee.....eeeeeee.....eeeeeeee........eeeeeeee.....eeeeeeee........eeeeee...eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5v3o C   47 INFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPD  428
                                    56        66        76        86        96       106       116       126|      142       152       162       172       182       192       202       221       231       241       251       261   ||  275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425   
                                                                                                         126|                                                                          210|                                          265|                                                                                                                                                              
                                                                                                          133                                                                           220                                           270                                                                                                                                                              

   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 5V3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V3O)

(-) Gene Ontology  (47, 53)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CRBN_HUMAN | Q96SW24m91 4tz4 5fqd 5hxb
        DDB1_HUMAN | Q165312b5l 2b5m 2b5n 2hye 3e0c 3ei1 3ei2 3ei3 3ei4 3i7h 3i7k 3i7l 3i7n 3i7o 3i7p 3i89 3i8c 3i8e 4a08 4a09 4a0a 4a0b 4a0k 4a0l 4a11 4ci1 4ci2 4ci3 4e54 4e5z 4tz4 5fqd 5hxb 5jk7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5V3O)