Structure of PDB 3wyj Chain A Binding Site BS01

Receptor Information
>3wyj Chain A (length=222) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIE
ALTLYAFSSPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNS
RLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQ
PDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTD
VLWPDFDEQDFEGALNAFANRE
Ligand information
Ligand IDH78
InChIInChI=1S/C34H36N2O18P4S2/c37-33(55(39,40)41,56(42,43)44)21-23-6-1-8-25(16-23)27-10-3-12-29(18-27)35-59(51,52)31-14-5-15-32(20-31)60(53,54)36-30-13-4-11-28(19-30)26-9-2-7-24(17-26)22-34(38,57(45,46)47)58(48,49)50/h1-20,35-38H,21-22H2,(H2,39,40,41)(H2,42,43,44)(H2,45,46,47)(H2,48,49,50)
InChIKeyUKSQFLAKPJZXNT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=S(=O)(Nc2cc(c1cccc(c1)CC(O)(P(=O)(O)O)P(=O)(O)O)ccc2)c3cccc(c3)S(=O)(=O)Nc5cc(c4cccc(c4)CC(O)(P(=O)(O)O)P(=O)(O)O)ccc5
OpenEye OEToolkits 1.7.6c1cc(cc(c1)c2cccc(c2)NS(=O)(=O)c3cccc(c3)S(=O)(=O)Nc4cccc(c4)c5cccc(c5)CC(O)(P(=O)(O)O)P(=O)(O)O)CC(O)(P(=O)(O)O)P(=O)(O)O
CACTVS 3.385OC(Cc1cccc(c1)c2cccc(N[S](=O)(=O)c3cccc(c3)[S](=O)(=O)Nc4cccc(c4)c5cccc(CC(O)([P](O)(O)=O)[P](O)(O)=O)c5)c2)([P](O)(O)=O)[P](O)(O)=O
FormulaC34 H36 N2 O18 P4 S2
Name[1-oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid
ChEMBLCHEMBL3410460
DrugBank
ZINCZINC000261173999
PDB chain3wyj Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wyj Antibacterial drug leads: DNA and enzyme multitargeting.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		M25 N28 G29 R39 A40 H43 A47 A69 F70 S71 L85 L88 F89
Binding residue
(residue number reindexed from 1)		M12 N15 G16 R26 A27 H30 A34 A56 F57 S58 L67 L70 F71
Annotation score1
Binding affinityMOAD: ic50=0.36uM
PDBbind-CN: -logKd/Ki=6.44,IC50=0.36uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D13 H30 L119
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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Biological Process
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Cellular Component
External links
PDB RCSB:3wyj, PDBe:3wyj, PDBj:3wyj
PDBsum3wyj
PubMed25574764
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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