Structure of PDB 4kn7 Chain X Binding Site BS01

Receptor Information
>4kn7 Chain X (length=517) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQV
MEEAPDADDTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVA
EYPEAITYLLEQYDRVEAEIDPELAREKFAELRAQYVVTRDTIKAKGRSH
ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCV
EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ
KLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK
KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED
KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA
ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA
KALRKLRHPSRSEVLRS
Ligand information
Ligand ID1RM
InChIInChI=1S/C56H70N6O13/c1-31-14-12-15-32(2)55(69)59-46-50(67)42-41(45-53(46)74-40-17-13-16-39(44(40)58-45)71-28-11-10-20-60-22-24-61(25-23-60)26-27-62-21-19-57-30-62)43-52(36(6)49(42)66)75-56(8,54(43)68)72-29-18-38(70-9)33(3)51(73-37(7)63)35(5)48(65)34(4)47(31)64/h12-19,21,29-31,33-35,38,47-48,51,64-66H,10-11,20,22-28H2,1-9H3,(H,59,69)/b14-12+,29-18+,32-15?/t31-,33+,34+,35+,38-,47-,48+,51+,56-/m0/s1
InChIKeyBWDTVIVNIJMQGS-DORLTJSWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=CC=C(C(=O)NC(=C5C3=Nc6c(cccc6OCCCCN7CCN(CC7)CCn8ccnc8)O5)C2=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
CACTVS 3.370CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4C(=O)C(=C5Oc6cccc(OCCCCN7CCN(CC7)CCn8ccnc8)c6N=C5c4c3C2=O)NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C
CACTVS 3.370CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4C(=O)C(=C5Oc6cccc(OCCCCN7CCN(CC7)CCn8ccnc8)c6N=C5c4c3C2=O)NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C
ACDLabs 12.01O=C8c7c1OC8(OC=CC(OC)C(C)C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)NC=2C(=O)c(c(O)c1C)c7C3=Nc6c(OC=23)cccc6OCCCCN5CCN(CCn4ccnc4)CC5)C)C)C
OpenEye OEToolkits 1.7.6Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)NC(=C5C3=Nc6c(cccc6OCCCCN7CCN(CC7)CCn8ccnc8)O5)C2=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC56 H70 N6 O13
NameBenzoxazinorifamycin-2c
ChEMBL
DrugBank
ZINC
PDB chain4kn7 Chain C Residue 1401 [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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PDB4kn7 X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins.
Resolution3.686 Å
Binding residue
(original residue number in PDB)		D513 D514 E515
Binding residue
(residue number reindexed from 1)		D421 D422 E423
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.62,IC50=24nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0005515 protein binding
GO:0016987 sigma factor activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006355 regulation of DNA-templated transcription
GO:0009408 response to heat
GO:0010468 regulation of gene expression
GO:0045892 negative regulation of DNA-templated transcription
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1903865 sigma factor antagonist complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4kn7, PDBe:4kn7, PDBj:4kn7
PDBsum4kn7
PubMed23679862
UniProtP00579|RPOD_ECOLI RNA polymerase sigma factor RpoD (Gene Name=rpoD)

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