Structure of PDB 2e9c Chain A Binding Site BS01

Receptor Information
>2e9c Chain A (length=208) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIE
ALTLYAFSSELDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTA
GNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVC
MHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGA
LNAFANRE
Ligand information
Ligand IDB75
InChIInChI=1S/C24H23NO9P2S/c26-24(35(27,28)29,36(30,31)32)16-17-5-3-8-19(13-17)20-9-4-10-22(14-20)25-37(33,34)23-12-11-18-6-1-2-7-21(18)15-23/h1-15,25-26H,16H2,(H2,27,28,29)(H2,30,31,32)
InChIKeyMZVWVRVNMXTDAK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(Cc1cccc(c1)c2cccc(N[S](=O)(=O)c3ccc4ccccc4c3)c2)([P](O)(O)=O)[P](O)(O)=O
ACDLabs 10.04O=S(=O)(Nc1cc(ccc1)c2cccc(c2)CC(O)(P(=O)(O)O)P(=O)(O)O)c4cc3ccccc3cc4
OpenEye OEToolkits 1.5.0c1ccc2cc(ccc2c1)S(=O)(=O)Nc3cccc(c3)c4cccc(c4)CC(O)(P(=O)(O)O)P(=O)(O)O
FormulaC24 H23 N O9 P2 S
Name1-HYDROXY-2-[3'-(NAPHTHALENE-2-SULFONYLAMINO)-BIPHENYL-3-YL]ETHYLIDENE-1,1-BISPHOSPHONIC ACID;
(1-HYDROXY-2-{3'-[(2-NAPHTHYLSULFONYL)AMINO]BIPHENYL-3-YL}ETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
ChEMBLCHEMBL259026
DrugBank
ZINCZINC000016051961
PDB chain2e9c Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2e9c Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases
Resolution2.05 Å
Binding residue
(original residue number in PDB)		M25 N28 G29 R39 H43 V50 A69 F70 S71 A142 A143
Binding residue
(residue number reindexed from 1)		M12 N15 G16 R26 H30 V37 A56 F57 S58 A110 A111
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D13 H30 L105
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2e9c, PDBe:2e9c, PDBj:2e9c
PDBsum2e9c
PubMed17535895
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

[Back to BioLiP]