Structure of PDB 6m1s Chain A Binding Site BS01

Receptor Information

>6m1s Chain A (length=187) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNSIDEALAGYCSEISITIH
TDESITVRDNGRGIPVDIHKEEGVSAAEVIMTVLHVGVSVVNALSHELRL
TIRRHNKVWEQVYHHGVPQFPLREVGETDGSGTEVHFKPSPETFSNIHFS
WDILAKRIRELSFLNSGVGILLRDERTGKEELFKYEG

Ligand information

Ligand ID

EZ9

InChI

InChI=1S/C26H23F4N7O3/c1-4-31-17-8-14(27)7-15-19-21(37-6-5-18(36-37)26(28,29)30)16(11-32-22(19)35-20(15)17)13-9-33-24(34-10-13)40-12-25(2,3)23(38)39/h5-11,31H,4,12H2,1-3H3,(H,32,35)(H,38,39)

InChIKey

KAPAQIUVYZBYAT-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.385	CCNc1cc(F)cc2c1[nH]c3ncc(c4cnc(OCC(C)(C)C(O)=O)nc4)c(n5ccc(n5)C(F)(F)F)c23
OpenEye OEToolkits 2.0.7	CCNc1cc(cc2c1[nH]c3c2c(c(cn3)c4cnc(nc4)OCC(C)(C)C(=O)O)n5ccc(n5)C(F)(F)F)F

Formula

C26 H23 F4 N7 O3

Name

3-[5-[8-(ethylamino)-6-fluoranyl-4-[3-(trifluoromethyl)pyrazol-1-yl]-9H-pyrido[2,3-b]indol-3-yl]pyrimidin-2-yl]oxy-2,2-dimethyl-propanoic acid

PDB chain

6m1s Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6m1s Discovery of Pyrido[2,3-b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV.
Resolution	2.254 Å
Binding residue (original residue number in PDB)	V45 N48 S49 E52 V73 D75 R78 I80 P81 I96 T167
Binding residue (residue number reindexed from 1)	V29 N32 S33 E36 V57 D59 R62 I64 P65 I80 T133
Annotation score	1
Binding affinity	MOAD: Ki<1nM

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

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Molecular Function

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Biological Process

External links

PDB	RCSB:6m1s, PDBe:6m1s, PDBj:6m1s
PDBsum	6m1s
PubMed	32787097
UniProt	Q9I7C2\|GYRB_PSEAE DNA gyrase subunit B (Gene Name=gyrB)

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