Structure of PDB 7vba Chain A Binding Site BS06

Receptor Information
>7vba Chain A (length=1473) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NMPWRRLQGISFGMYSAEELKKLSVKSITNPRYLDSLGNPSANGLYDLAL
GPADSKEVCSTCVQDFSNCSGHLGHIELPLTVYNPLLFDKLYLLLRGSCL
NCHMLTCPRAVIHLLLCQLRVLEVGALQAVYELERILNRFIREELEQYTT
EIVQNNLLGSQGAHVKNVCESKSKLIALFWKAHMNAKRCPHCKTGRSVVR
KEHNSKLTITFRGYLTPTSAREHLSALWKNEGFFLNYLFSRFNPSVFFLD
FLVVPPSRYRPVSRLGDQMFTNGQTVNLQAVMKDVVLIRKLLALMAQEQS
LIDKLYNIWIRLQSHVNIVFDSEMDKLMMDKYPGIRQILEKKEGLFRKHM
MGKRVDYAARSVICPDMYINTNEIGIPMVFATKLTYPQPVTPWNVQELRQ
AVINGPNVHPGASMVINEDGSRTALSAVDMTQREAVAKQLLTQGTKIVCR
HVKNGDILLLNRQPTLHRPSIQAHRARILPEEKVLRLHYANCKAYNADFD
GDEMNAHFPQSELGRAEAYVLACTDQQYLVPKDGQPLAGLIQDHMVSGAS
MTTRGCFFTREHYMELVYRGLTDKVGRVKLLSPSILKPFPLWTGKQVVST
LLINIIPEDHIPLNLSGKAKITGKAWVKETPRSVPGFNPDSMCESQVIIR
EGELLCGVLDKAHYGSSAYGLVHCCYEIYGGETSGKVLTCLARLFTAYLQ
LYRGFTLGVEDILVKPKADVKRQRIIEESTHCGPQAVRAALNLPEAASYD
EVRGKWQDAHLGKDQRDFNMIDLKFKEEVNHYSNEINKACMPFGLHRQFP
ENSLQMMVQSGAKGSTVNTMQISCLLGQIELEGRRPPLMASGKSLPCFEP
YEFTPRAGGFVTGRFLTGIKPPEFFFHCMAGREGLVDTAVKTSRSGYLQR
CIIKHLEGLVVQYDLTVRDSDGSVVQFLYGEDGLDIPKTQFLQPKQFPFL
ASNYEVIMKSQHLHEVLSRADPKKALHHFRAIKKWQSKHPNTLLRRGAFL
SYSQKIQEAVKALKLESENRNGRSPGTQEMLRMWYELDEESRRKYQKKAA
ACPDPSLSVWRPDIYFASVSETFETKVDDYSQEWAAQTEKSYEKSELSLD
RLRTLLQLKWQRSLCEPGEAVGLLAAQSIGEPSTQMMNVTLGIPRLREIL
MVASANIKTPMMSVPVLNTKKALKRVKSLKKQLTRVCLGEVLQKIDVQEQ
VYQLRFQFLPHAYYQQEKCLRPEDILRFMETRFFKLLMESIKKKNNKASE
AMERRVQAVREIHPFIDDYQYDTEESLWCQVTVKLPLMKINFDMSSLVVS
LAHGAVIYATKGITRCLLNETTNNKNEKELVLNTEGINLPELFKYAEVLD
LRRLYSNDIHAIANTYGIEAALRVIEKEIKDVFAVYGIAVDPRHLSLVAD
YMCFEGVYKPLNRFGIRSNSSPLQQMTFETSFQFLKQATMLGSHDELRSP
SACLVVGKVVRGGTGLFELKQPL
Ligand information
Ligand ID2TM
InChIInChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
InChIKeySTGUOVSTMBLHFT-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine;
CMPcPP
ChEMBL
DrugBank
ZINCZINC000098208273
PDB chain7vba Chain A Residue 2004 [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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PDB7vba Structure of the human RNA polymerase I elongation complex.
Resolution2.89 Å
Binding residue
(original residue number in PDB)		R552 P554
Binding residue
(residue number reindexed from 1)		R462 P464
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001054 RNA polymerase I activity
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003899 DNA-directed 5'-3' 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
GO:0071667 DNA/RNA hybrid binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006360 transcription by RNA polymerase I
GO:1904750 negative regulation of protein localization to nucleolus
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005736 RNA polymerase I complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7vba, PDBe:7vba, PDBj:7vba
PDBsum7vba
PubMed34671025
UniProtO95602|RPA1_HUMAN DNA-directed RNA polymerase I subunit RPA1 (Gene Name=POLR1A)

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