Structure of PDB 9bbh Chain A Binding Site BS01

Receptor Information
>9bbh Chain A (length=1104) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLR
PVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDI
ITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNK
ELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREK
EFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAP
PIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAM
ETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHA
SIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMG
FVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISV
ASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSN
GLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVF
ACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLT
IGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQGTTALRP
SASTQALSSSVSSSEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSC
KLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGA
VYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGD
FILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAE
NAFNLFVCQKDSTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQTPTQGSV
LFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHT
ERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQREATADDLIKVVEEL
TRIH
Ligand information
Ligand IDVVP
InChIInChI=1S/C9H9NO/c1-11-9-4-2-3-8-7(9)5-6-10-8/h2-6,10H,1H3
InChIKeyLUNOXNMCFPFPMO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cccc2c1cc[nH]2
CACTVS 3.385COc1cccc2[nH]ccc12
ACDLabs 12.01n1ccc2c1cccc2OC
FormulaC9 H9 N O
Name4-methoxy-1H-indole
ChEMBLCHEMBL2018155
DrugBank
ZINCZINC000000407091
PDB chain9bbh 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB9bbh Co-crystal structure of human DDB1 bound to fragment UB028670
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K35 Y42 S331 F353
Binding residue
(residue number reindexed from 1)		K35 Y42 S331 F353
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:9bbh, PDBe:9bbh, PDBj:9bbh
PDBsum9bbh
PubMed
UniProtQ16531|DDB1_HUMAN DNA damage-binding protein 1 (Gene Name=DDB1)

[Back to BioLiP]