Structure of PDB 4y7n Chain A Binding Site BS06

Receptor Information
>4y7n Chain A (length=1393) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCDVPS
LVSRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTSL
GFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKA
NISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPV
KSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAK
TLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAG
DIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNL
SVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG
IVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLW
SGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTV
GSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIAD
GPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFL
NEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEG
KRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGRE
GLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDG
MDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGD
LKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFH
IDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLL
RSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSI
GEPATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAK
LIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWL
LRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRV
VAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEP
EWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEV
YNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSF
EETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI
Ligand information
Ligand IDG2P
InChIInChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-30(20,21)3-31(22,23)29-32(24,25)26/h2,4,6-7,10,17-18H,1,3H2,(H,20,21)(H,22,23)(H2,24,25,26)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
InChIKeyGXTIEXDFEKYVGY-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(C[P@@](=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O13 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
ChEMBLCHEMBL1232908
DrugBankDB03532
ZINCZINC000016051609
PDB chain4y7n Chain T Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4y7n Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		R446 P448 N479 T831
Binding residue
(residue number reindexed from 1)		R424 P426 N457 T809
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D459 D461 D463
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:4y7n, PDBe:4y7n, PDBj:4y7n
PDBsum4y7n
PubMed26123024
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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