Structure of PDB 3sgv Chain B Binding Site BS01

Receptor Information
>3sgv Chain B (length=217) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGI
EALTLYAFVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQER
IRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQID
EEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPD
FDEQDFEGALNAFANRE
Ligand information
Ligand ID2BJ
InChIInChI=1S/C22H18N2O6/c1-13-6-8-18(10-14(13)2)30-17-5-3-4-15(11-17)23-21(25)20-12-16(24(28)29)7-9-19(20)22(26)27/h3-12H,1-2H3,(H,23,25)(H,26,27)
InChIKeyGQGBAJUULMBPOF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cc1ccc(Oc2cccc(NC(=O)c3cc(ccc3C(O)=O)[N+]([O-])=O)c2)cc1C
OpenEye OEToolkits 1.7.2Cc1ccc(cc1C)Oc2cccc(c2)NC(=O)c3cc(ccc3C(=O)O)[N+](=O)[O-]
ACDLabs 12.01[O-][N+](=O)c1cc(c(C(=O)O)cc1)C(=O)Nc3cccc(Oc2ccc(c(c2)C)C)c3
FormulaC22 H18 N2 O6
Name2-{[3-(3,4-dimethylphenoxy)phenyl]carbamoyl}-4-nitrobenzoic acid
ChEMBL
DrugBank
ZINCZINC000095921142
PDB chain3sgv Chain B Residue 5001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3sgv Antibacterial drug leads targeting isoprenoid biosynthesis.
Resolution1.61 Å
Binding residue
(original residue number in PDB)		K44 A47 K48 V50 R51 L88 A92 E96
Binding residue
(residue number reindexed from 1)		K32 A35 K36 V38 R39 L65 A69 E73
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.46,IC50=35uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D14 H31 L114
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:3sgv, PDBe:3sgv, PDBj:3sgv
PDBsum3sgv
PubMed23248302
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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