Structure of PDB 9bbe Chain A Binding Site BS01

Receptor Information
>9bbe Chain A (length=1106) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRP
VKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDII
TRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKE
LKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKE
FNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPP
IIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLR
VELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAME
TFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHAS
IDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGF
VDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVA
SCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNG
LSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHY
LLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFA
CSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTI
GTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQGTTALRPS
ASTQALSSSVSSEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL
GKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVY
SMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFI
LVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENA
FNLFVCQKDSTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQTPTQGSVLF
GTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDMKREATADDLIKVVE
ELTRIH
Ligand information
Ligand IDA1AK9
InChIInChI=1S/C13H15N3O2/c1-17-11-4-2-9(3-5-11)13-15-12(16-18-13)10-6-7-14-8-10/h2-5,10,14H,6-8H2,1H3/t10-/m0/s1
InChIKeyLCPXGPRZJSMWFF-JTQLQIEISA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1)c2onc(n2)[C@H]3CCNC3
OpenEye OEToolkits 2.0.7COc1ccc(cc1)c2nc(no2)C3CCNC3
OpenEye OEToolkits 2.0.7COc1ccc(cc1)c2nc(no2)[C@H]3CCNC3
CACTVS 3.385COc1ccc(cc1)c2onc(n2)[CH]3CCNC3
ACDLabs 12.01COc1ccc(cc1)c1nc(no1)C1CNCC1
FormulaC13 H15 N3 O2
Name5-(4-methoxyphenyl)-3-[(3S)-pyrrolidin-3-yl]-1,2,4-oxadiazole
ChEMBL
DrugBank
ZINC
PDB chain9bbe Chain A Residue 1203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB9bbe Co-crystal structure of human DDB1 bound to fragment UB028668
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E72 L76 I88 E90 R103 D146 N149
Binding residue
(residue number reindexed from 1)		E71 L75 I87 E89 R102 D145 N148
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0005515 protein binding
GO:0030674 protein-macromolecule adaptor activity
GO:0044877 protein-containing complex binding
GO:0071987 WD40-repeat domain binding
GO:0097602 cullin family protein binding
GO:0160072 ubiquitin ligase complex scaffold activity
Biological Process
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0007056 spindle assembly involved in female meiosis
GO:0010498 proteasomal protein catabolic process
GO:0016055 Wnt signaling pathway
GO:0016567 protein ubiquitination
GO:0019076 viral release from host cell
GO:0034644 cellular response to UV
GO:0035234 ectopic germ cell programmed cell death
GO:0042752 regulation of circadian rhythm
GO:0043066 negative regulation of apoptotic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0044725 epigenetic programming in the zygotic pronuclei
GO:0045070 positive regulation of viral genome replication
GO:0045722 positive regulation of gluconeogenesis
GO:0045732 positive regulation of protein catabolic process
GO:0046726 positive regulation by virus of viral protein levels in host cell
GO:0048511 rhythmic process
GO:0051093 negative regulation of developmental process
GO:0051702 biological process involved in interaction with symbiont
GO:0070914 UV-damage excision repair
GO:1901990 regulation of mitotic cell cycle phase transition
GO:2000242 negative regulation of reproductive process
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex
GO:0031465 Cul4B-RING E3 ubiquitin ligase complex
GO:0032991 protein-containing complex
GO:0035861 site of double-strand break
GO:0070062 extracellular exosome
GO:0080008 Cul4-RING E3 ubiquitin ligase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:9bbe, PDBe:9bbe, PDBj:9bbe
PDBsum9bbe
PubMed
UniProtQ16531|DDB1_HUMAN DNA damage-binding protein 1 (Gene Name=DDB1)

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