Structure of PDB 8qk2 Chain A Binding Site BS03

Receptor Information
>8qk2 Chain A (length=230) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATLFIADLHLQTEEPEITAGFLRFLQGEARQADALYILGDLFEAWIGDDD
PNPLHQQIASAIKAVVDAGVPCYFIHGNRDFLVGQRFARQSGMILLAEEE
RLDLYGREVLIMHGDTLCTDDQGYLAFRAKVHTPWIQRLFLALPLFIRHR
IAARMRAEIMDVNPQAVVDAMERHHVQWLIHGHTHRPAVHELQANGQPAW
RVVLGAWHSEGSMVKVTPDDVELIHFPFHH
Ligand information
Ligand IDVTF
InChIInChI=1S/C25H27N7O5S2/c1-18-16-20(17-26)29-25(27-18)31-12-14-32(15-13-31)39(36,37)21-10-8-19(9-11-21)28-24(33)22-6-4-5-7-23(22)30(2)38(3,34)35/h4-11,16H,12-15H2,1-3H3,(H,28,33)
InChIKeyGYNDUARBATVDGK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(c1ccccc1C(=O)Nc2ccc(cc2)[S](=O)(=O)N3CCN(CC3)c4nc(C)cc(n4)C#N)[S](C)(=O)=O
OpenEye OEToolkits 2.0.7Cc1cc(nc(n1)N2CCN(CC2)S(=O)(=O)c3ccc(cc3)NC(=O)c4ccccc4N(C)S(=O)(=O)C)C#N
FormulaC25 H27 N7 O5 S2
Name~{N}-[4-[4-(4-cyano-6-methyl-pyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide
ChEMBL
DrugBank
ZINC
PDB chain8qk2 Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8qk2 Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		A45 W46 N79 R80 F82 Y125 F128 F141 M156
Binding residue
(residue number reindexed from 1)		A44 W45 N78 R79 F81 Y124 F127 F140 M155
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.54: UDP-2,3-diacylglucosamine diphosphatase.
Gene Ontology
Molecular Function
GO:0008758 UDP-2,3-diacylglucosamine hydrolase activity
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0019897 extrinsic component of plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8qk2, PDBe:8qk2, PDBj:8qk2
PDBsum8qk2
PubMed38579010
UniProtA6T5R0|LPXH_KLEP7 UDP-2,3-diacylglucosamine hydrolase (Gene Name=lpxH)

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