Structure of PDB 6y8n Chain A Binding Site BS01

Receptor Information
>6y8n Chain A (length=183) Species: 1797 (Mycolicibacterium thermoresistibile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGHATKVRVRL
LADGGVEVSDDGRGIPVEMHESGVPTVDVVMTQVGVSVVNALSTRMEVEI
CRDGYQWFQTYDKSVPGTLKQGEKTRKTGTVVRFWPDPDVFETTTFDFET
VARRLQEQAFLNKGLTIELIDERDGKHRTFYYP
Ligand information
Ligand IDOGH
InChIInChI=1S/C21H21FN8O/c1-9-25-5-11(6-26-9)31-21-28-19-16(12-3-10(22)4-15(24-2)18(12)27-19)20(29-21)30-7-13-14(8-30)17(13)23/h3-6,13-14,17,24H,7-8,23H2,1-2H3,(H,27,28,29)/t13-,14+,17+
InChIKeyGOOKXTQTAFDVNH-HALDLXJZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1cc(F)cc2c1[nH]c3nc(Oc4cnc(C)nc4)nc(N5C[CH]6C(N)[CH]6C5)c23
OpenEye OEToolkits 2.0.7Cc1ncc(cn1)Oc2nc3c(c4cc(cc(c4[nH]3)NC)F)c(n2)N5CC6C(C5)C6N
CACTVS 3.385CNc1cc(F)cc2c1[nH]c3nc(Oc4cnc(C)nc4)nc(N5C[C@H]6C(N)[C@H]6C5)c23
OpenEye OEToolkits 2.0.7Cc1ncc(cn1)Oc2nc3c(c4cc(cc(c4[nH]3)NC)F)c(n2)N5C[C@@H]6[C@H](C5)C6N
FormulaC21 H21 F N8 O
Name4-[(1~{S},5~{R})-6-azanyl-3-azabicyclo[3.1.0]hexan-3-yl]-6-fluoranyl-~{N}-methyl-2-(2-methylpyrimidin-5-yl)oxy-9~{H}-pyrimido[4,5-b]indol-8-amine
ChEMBL
DrugBank
ZINC
PDB chain6y8n Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6y8n Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		N52 A53 E56 V77 D79 R82 I84 P85 T169 V171
Binding residue
(residue number reindexed from 1)		N33 A34 E37 V58 D60 R63 I65 P66 T130 V132
Annotation score1
Binding affinityMOAD: ic50=9nM
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6y8n, PDBe:6y8n, PDBj:6y8n
PDBsum6y8n
PubMed32728686
UniProtG7CIP8

[Back to BioLiP]