Structure of PDB 5cqj Chain A Binding Site BS01

Receptor Information
>5cqj Chain A (length=212) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGI
EALTLYAFELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSE
ALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLN
QHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQD
FEGALNAFANRE
Ligand information
Ligand ID53Q
InChIInChI=1S/C26H28ClNO/c1-3-28(4-2)19-20-29-24-17-15-22(16-18-24)25(21-11-7-5-8-12-21)26(27)23-13-9-6-10-14-23/h5-18H,3-4,19-20H2,1-2H3/b26-25+
InChIKeyGKIRPKYJQBWNGO-OCEACIFDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCN(CC)CCOc1ccc(cc1)C(=C(c2ccccc2)Cl)c3ccccc3
ACDLabs 12.01C(Oc1ccc(cc1)\C(=C(/c2ccccc2)Cl)c3ccccc3)CN(CC)CC
CACTVS 3.385CCN(CC)CCOc1ccc(cc1)C(=C(Cl)c2ccccc2)c3ccccc3
OpenEye OEToolkits 2.0.7CCN(CC)CCOc1ccc(cc1)/C(=C(\c2ccccc2)/Cl)/c3ccccc3
CACTVS 3.385CCN(CC)CCOc1ccc(cc1)\C(=C(Cl)/c2ccccc2)c3ccccc3
FormulaC26 H28 Cl N O
NameClomifene;
1-[(E)-2-chloro-1,2-diphenylethenyl]-4-methoxybenzene;
clomiphene
ChEMBLCHEMBL954
DrugBankDB06735
ZINCZINC000001530601
PDB chain5cqj 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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PDB5cqj Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		A47 A92 E96
Binding residue
(residue number reindexed from 1)		A35 A64 E68
Annotation score1
Binding affinityMOAD: ic50=15.4uM
PDBbind-CN: -logKd/Ki=4.81,IC50=15.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D14 H31 L109
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:5cqj, PDBe:5cqj, PDBj:5cqj
PDBsum5cqj
PubMed26283394
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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