Structure of PDB 4h2o Chain B Binding Site BS02

Receptor Information
>4h2o Chain B (length=208) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIE
ALTLYAFSSFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEA
LTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGQPDQIDEEMLNQHV
CMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEG
ALNAFANR
Ligand information
Ligand ID0YW
InChIInChI=1S/C24H30N2O6/c1-2-3-4-5-6-7-8-9-15-32-20-12-10-11-18(16-20)23(27)25-22-14-13-19(26(30)31)17-21(22)24(28)29/h10-14,16-17H,2-9,15H2,1H3,(H,25,27)(H,28,29)
InChIKeyPZXIQAYPKSOMHD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01[O-][N+](=O)c1ccc(c(C(=O)O)c1)NC(=O)c2cc(OCCCCCCCCCC)ccc2
OpenEye OEToolkits 1.7.6CCCCCCCCCCOc1cccc(c1)C(=O)Nc2ccc(cc2C(=O)O)[N+](=O)[O-]
CACTVS 3.370CCCCCCCCCCOc1cccc(c1)C(=O)Nc2ccc(cc2C(O)=O)[N+]([O-])=O
FormulaC24 H30 N2 O6
Name2-{[3-(decyloxy)benzoyl]amino}-5-nitrobenzoic acid
ChEMBL
DrugBank
ZINCZINC000098207899
PDB chain4h2o Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4h2o Antibacterial drug leads targeting isoprenoid biosynthesis.
Resolution2.14 Å
Binding residue
(original residue number in PDB)		R51 F89 E96 N144
Binding residue
(residue number reindexed from 1)		R38 F60 E67 N115
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.52,IC50=3.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D13 H30 L108
Enzyme Commision number 2.5.1.31: ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl- diphosphate specific].
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008834 di-trans,poly-cis-undecaprenyl-diphosphate synthase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0036094 small molecule binding
GO:0042803 protein homodimerization activity
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0016094 polyprenol biosynthetic process
GO:0043164 Gram-negative-bacterium-type cell wall biogenesis
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4h2o, PDBe:4h2o, PDBj:4h2o
PDBsum4h2o
PubMed23248302
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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