Structure of PDB 7kee Chain A Binding Site BS06

Receptor Information
>7kee Chain A (length=1390) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCELVS
RGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTSLGFN
EVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANIS
LETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSI
RARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLT
YPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQ
LQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVT
SPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQ
DTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGK
QILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSS
NGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPT
MREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEA
RDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRI
AFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLI
DTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDA
AHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKL
QVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDH
TKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSR
LATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEP
ATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIR
SAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWLLRL
ELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVAE
EDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWV
LETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNV
IASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEET
VEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI
Ligand information
Ligand IDWCG
InChIInChI=1S/C16H21O14P3/c1-26-12-7-10-5-3-2-4-9(10)6-11(12)16-15(18)14(17)13(28-16)8-27-32(22,23)30-33(24,25)29-31(19,20)21/h2-7,13-18H,8H2,1H3,(H,22,23)(H,24,25)(H2,19,20,21)/t13-,14-,15-,16+/m1/s1
InChIKeyCCJNXXZRNQFAFA-FPCVCCKLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cc2ccccc2cc1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 2.0.7COc1cc2ccccc2cc1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385COc1cc2ccccc2cc1[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385COc1cc2ccccc2cc1[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01COc2cc1ccccc1cc2C3C(C(C(COP(=O)(O)OP(O)(=O)OP(O)(O)=O)O3)O)O
FormulaC16 H21 O14 P3
Name(1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol
ChEMBL
DrugBank
ZINC
PDB chain7kee Chain B Residue 2101 [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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PDB7kee Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		N479 D481 K752
Binding residue
(residue number reindexed from 1)		N454 D456 K727
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7kee, PDBe:7kee, PDBj:7kee
PDBsum7kee
PubMed34140682
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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