Structure of PDB 6nj0 Chain A Binding Site BS01

Receptor Information
>6nj0 Chain A (length=439) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IFSDWPWRHWRQVRGETIALRLNDEQLNWRELCARVDELASGFAVQGVVE
GSGVMLRAWNTPQTLLAWLALLQCGARVLPVNPQLPQPLLEELLPNLTLQ
FALVPGENTFPALTSLHIQLVEGAHAATWQPTRLCSMTLTSGLPKAAVHT
YQAHLASAQGVLSLIPFGDHDDWLLSLPLFHVSGQGIMWRWLYAGARMTV
RDKQPLEQMLAGCTHASLVPTQLWRLLVNRSSVSLKAVLLGGAAIPVELT
EQAREQGIRCFCGYGLTEFASTVCAKEADLADVGSPLPGREVKIVNNEVW
LRAASMAEGYWRNGQLVSLVNDEGWYATRDRGEMHNGKLTIVGRLDNLFF
SGGEGIQPEEVERVIAAHPAVLQVFIVPVADKEFGHRPVAVMEYDHESVD
LSEWVKDKLARFQQPVRWLTLPPELKNSRQALKEWVQRQ
Ligand information
Ligand IDKOY
InChIInChI=1S/C26H25N5O7/c27-23-20-24(29-12-28-23)31(13-30-20)25-22(34)21(33)19(38-25)11-37-15-5-3-4-14(10-15)8-9-18(32)16-6-1-2-7-17(16)26(35)36/h1-7,10,12-13,19,21-22,25,33-34H,8-9,11H2,(H,35,36)(H2,27,28,29)/t19-,21-,22-,25-/m1/s1
InChIKeyGEMGRSMVWNUQGG-PTGPVQHPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c12n(cnc1c(ncn2)N)C5OC(COc4cc(CCC(c3c(C(O)=O)cccc3)=O)ccc4)C(O)C5O
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(=O)CCc2cccc(c2)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)C(=O)O
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COc4cccc(CCC(=O)c5ccccc5C(O)=O)c4)[C@@H](O)[C@H]3O
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(=O)CCc2cccc(c2)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)C(=O)O
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](COc4cccc(CCC(=O)c5ccccc5C(O)=O)c4)[CH](O)[CH]3O
FormulaC26 H25 N5 O7
Name5'-O-{3-[3-(2-carboxyphenyl)-3-oxopropyl]phenyl}adenosine
ChEMBL
DrugBank
ZINC
PDB chain6nj0 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6nj0 Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		L182 S188 R195 L223 L244 G246 A248 A249 G268 Y269 G270 T272 S276 T277 V289 D336 R350
Binding residue
(residue number reindexed from 1)		L177 S183 R190 L218 L239 G241 A243 A244 G263 Y264 G265 T267 S271 T272 V283 D330 R344
Annotation score2
Binding affinityMOAD: ic50=8.1uM
PDBbind-CN: -logKd/Ki=6.61,Kd=244nM
Enzymatic activity
Catalytic site (original residue number in PDB) T142 E273 F356 G361
Catalytic site (residue number reindexed from 1) T140 E268 F350 G355
Enzyme Commision number 6.2.1.26: o-succinylbenzoate--CoA ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008756 o-succinylbenzoate-CoA ligase activity
GO:0016874 ligase activity
GO:0016877 ligase activity, forming carbon-sulfur bonds
GO:0042802 identical protein binding
Biological Process
GO:0009234 menaquinone biosynthetic process
Cellular Component
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6nj0, PDBe:6nj0, PDBj:6nj0
PDBsum6nj0
PubMed30912442
UniProtP37353|MENE_ECOLI 2-succinylbenzoate--CoA ligase (Gene Name=menE)

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