Structure of PDB 2e9d Chain A Binding Site BS01

Receptor Information
>2e9d Chain A (length=218) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEAL
TLYAFSAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQE
RIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQI
DEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWP
DFDEQDFEGALNAFANRE
Ligand information
Ligand IDB76
InChIInChI=1S/C20H20O8P2/c21-20(29(22,23)24,30(25,26)27)14-28-19-11-5-10-18(13-19)17-9-4-8-16(12-17)15-6-2-1-3-7-15/h1-13,21H,14H2,(H2,22,23,24)(H2,25,26,27)
InChIKeyNWIARQRYIRVYCM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(COc1cccc(c1)c2cccc(c2)c3ccccc3)([P](O)(O)=O)[P](O)(O)=O
OpenEye OEToolkits 1.5.0c1ccc(cc1)c2cccc(c2)c3cccc(c3)OCC(O)(P(=O)(O)O)P(=O)(O)O
ACDLabs 10.04O=P(O)(O)C(O)(COc1cc(ccc1)c3cccc(c2ccccc2)c3)P(=O)(O)O
FormulaC20 H20 O8 P2
Name[1-HYDROXY-2-(1,1':3',1''-TERPHENYL-3-YLOXY)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)
ChEMBLCHEMBL260880
DrugBankDB07426
ZINCZINC000016051964
PDB chain2e9d Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2e9d Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N28 H43 F70 S71
Binding residue
(residue number reindexed from 1)		N13 H28 F55 S56
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.89,IC50=1.3uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D11 H28 L115
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:2e9d, PDBe:2e9d, PDBj:2e9d
PDBsum2e9d
PubMed17535895
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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