Structure of PDB 4h38 Chain A Binding Site BS01

Receptor Information
>4h38 Chain A (length=214) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEA
LTLYAFSSLMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRK
SEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEM
LNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDE
QDFEGALNAFANRE
Ligand information
Ligand ID0YX
InChIInChI=1S/C21H28BrO5P/c1-2-3-4-5-6-7-13-26-19-10-8-9-17(14-19)16-27-20-12-11-18(22)15-21(20)28(23,24)25/h8-12,14-15H,2-7,13,16H2,1H3,(H2,23,24,25)
InChIKeyXTZIHTNEICPHNT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCCCCOc1cccc(c1)COc2ccc(cc2P(=O)(O)O)Br
ACDLabs 12.01Brc2cc(c(OCc1cccc(OCCCCCCCC)c1)cc2)P(=O)(O)O
CACTVS 3.370CCCCCCCCOc1cccc(COc2ccc(Br)cc2[P](O)(O)=O)c1
FormulaC21 H28 Br O5 P
Name(5-bromo-2-{[3-(octyloxy)benzyl]oxy}phenyl)phosphonic acid
ChEMBL
DrugBank
ZINCZINC000098207900
PDB chain4h38 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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PDB4h38 Antibacterial drug leads targeting isoprenoid biosynthesis.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		A47 V50 R51 A92 L93 E96 S99 L100
Binding residue
(residue number reindexed from 1)		A33 V36 R37 A66 L67 E70 S73 L74
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.04,IC50=0.92uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D12 H29 L111
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:4h38, PDBe:4h38, PDBj:4h38
PDBsum4h38
PubMed23248302
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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