Structure of PDB 5c5h Chain A Binding Site BS02

Receptor Information
>5c5h Chain A (length=443) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMIFSDWPWRHWRQVRGETIALRLNDEQLNWRELCARVDELASGFAVQG
VVEGSGVMLRAWNTPQTLLAWLALLQCGARVLPVNPQLPQPLLEELLPNL
TLQFALVPDGENTFPALTSLHIQLVEGAHAATWQPTRLCSMTLTSSTGLP
KAAVHTYQAHLASAQGVLSLIPFGDHDDWLLSLPLFHVSGQGIMWKWLYA
GARMTVRDKQPLEQMLAGCTHASLVPTQLWRLLVNRSSVSLKAVLLGGAA
IPVELTEQAREQGIRCFCGYGLTEFASTVCAKEADGLADVGSPLPGREVK
IVNNEVWLRAASMAEGYWRNGQLVSLVNDEGWYATRDRGEMHNGKLTIVG
RLDNLFFSGGEGIQPEEVERVIAAHPAVLQVFIVPVADKFGHRPVAVMEY
DHESVDLSEWVKDKLARFQQPVRWLTLPPKISRQALKEWVQRQ
Ligand information
Ligand ID4YB
InChIInChI=1S/C21H22N6O10S/c22-18-15-19(24-8-23-18)27(9-25-15)20-17(31)16(30)13(37-20)7-36-38(34,35)26-14(29)6-5-12(28)10-3-1-2-4-11(10)21(32)33/h1-4,8-9,13,16-17,20,30-31H,5-7H2,(H,26,29)(H,32,33)(H2,22,23,24)/t13-,16-,17-,20-/m1/s1
InChIKeyJRKRGBFWNBVHHH-AEVYOOLXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(c(c1)C(=O)CCC(=O)NS(=O)(=O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)C(=O)O
OpenEye OEToolkits 1.9.2c1ccc(c(c1)C(=O)CCC(=O)NS(=O)(=O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)C(=O)O
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[S](=O)(=O)NC(=O)CCC(=O)c4ccccc4C(O)=O)[CH](O)[CH]3O
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)CCC(=O)c4ccccc4C(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01c12ncnc(c1ncn2C4OC(COS(NC(CCC(c3c(C(=O)O)cccc3)=O)=O)(=O)=O)C(O)C4O)N
FormulaC21 H22 N6 O10 S
Name5'-O-{[4-(2-carboxyphenyl)-4-oxobutanoyl]sulfamoyl}adenosine
ChEMBL
DrugBank
ZINCZINC000200180122
PDB chain5c5h Chain A Residue 502 [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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PDB5c5h Mechanism of MenE Inhibition by Acyl-Adenylate Analogues and Discovery of Novel Antibacterial Agents.
Resolution2.401 Å
Binding residue
(original residue number in PDB)		S188 L223 L244 G246 G247 A248 A249 Y269 G270 L271 T272 S276 T277 D336 I347 K437
Binding residue
(residue number reindexed from 1)		S189 L224 L245 G247 G248 A249 A250 Y270 G271 L272 T273 S277 T278 D337 I348 K430
Annotation score2
Binding affinityMOAD: Kd=394nM
PDBbind-CN: -logKd/Ki=6.40,Kd=394nM
Enzymatic activity
Catalytic site (original residue number in PDB) T142 S162 H186 G270 E273 F356 G361
Catalytic site (residue number reindexed from 1) T144 S163 H187 G271 E274 F357 G362
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:5c5h, PDBe:5c5h, PDBj:5c5h
PDBsum5c5h
PubMed26394156
UniProtP37353|MENE_ECOLI 2-succinylbenzoate--CoA ligase (Gene Name=menE)

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