Structure of PDB 6gau Chain B Binding Site BS01

Receptor Information
>6gau Chain B (length=1068) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRG
IPVATHASGIPTVDVVMTQLGVSVVNALSTRLEVEIKRDGYEWSQVYEKS
EPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKG
LTINLTDERVTQDEVVDEVVSDVAEAPVKSRTFHYPGGLVDFVKHINRTK
NAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEE
GFRSALTSVVNKYAKDRGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTE
VKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAARKSATDIGG
LPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIIN
VEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDG
QHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRER
DGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVT
LDDAAAADELFSILMGEDVDARRSFITRNAKDIEPVDIEQEMQRSYIDYA
MSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMG
NYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEA
RLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIA
VGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAG
LIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDN
FITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLY
KHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLR
KANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQA
QAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDE
LAEIVDRHGDDRRTRIIA
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain6gau Chain B Residue 1601 [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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PDB6gau Overall Structures of Mycobacterium tuberculosis DNA Gyrase Reveal the Role of a Corynebacteriales GyrB-Specific Insert in ATPase Activity.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		N52 G83 I84 V99 G124 V125
Binding residue
(residue number reindexed from 1)		N19 G50 I51 V66 G71 V72
Annotation score4
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0034335 DNA negative supercoiling activity
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006261 DNA-templated DNA replication
GO:0006265 DNA topological change
GO:0046677 response to antibiotic
Cellular Component
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6gau, PDBe:6gau, PDBj:6gau
PDBsum6gau
PubMed30744994
UniProtP9WG45|GYRB_MYCTU DNA gyrase subunit B (Gene Name=gyrB);
P9WG47|GYRA_MYCTU DNA gyrase subunit A (Gene Name=gyrA)

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