Structure of PDB 5x8f Chain D Binding Site BS01

Receptor Information
>5x8f Chain D (length=484) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTEQPNWLMQRAQLTPERIALIYEDQTVTFAELFAASKRMAEQLAAHSVR
KGDTAAILLQNRAEMVYAVHACFLLGVKAVLLNTKLSTHERLFQLEDSGS
GFLLTDSSFEKKEYEHIVQTIDVDELMKEAAEEIEIEAYMQMDATATLMY
TSGTTGKPKGVQQTFGNHYFSAVSSALNLGITEQDRWLIALPLFHISGLS
ALFKSVIYGMTVVLHQRFSVSDVLHSINRHEVTMISAVQTMLASLLEETN
RCPESIRCILLGGGPAPLPLLEECREKGFPVFQSYGMTETCSQIVTLSPE
FSMEKLGSAGKPLFSCEIKIERDGQVCEPYEHGEIMVKGPNVMKSYFNRE
SANEASFQNGWLKTGDLGYLDNEGFLYVLDRRSDLIISGGENIYPAEVES
VLLSHPAVAEAGVSGAEDKKWGKVPHAYLVLHKPVSAGELTDYCKERLAK
YKRPKKFFVLDRLPRNASNKLLRNQLKDARKGEL
Ligand information
Ligand IDS0N
InChIInChI=1S/C32H45N8O20P3/c1-32(2,26(45)29(46)36-10-9-22(43)35-12-11-34-21(42)8-7-19(41)17-5-3-4-6-18(17)31(47)48)14-57-63(54,55)60-62(52,53)56-13-20-25(59-61(49,50)51)24(44)30(58-20)40-16-39-23-27(33)37-15-38-28(23)40/h3-6,15-16,20,24-26,30,44-45H,7-14H2,1-2H3,(H,34,42)(H,35,43)(H,36,46)(H,47,48)(H,52,53)(H,54,55)(H2,33,37,38)(H2,49,50,51)/t20-,24-,25-,26+,30-/m1/s1
InChIKeyQCTNXUGGWNSKFY-HSJNEKGZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(O)=O
OpenEye OEToolkits 1.7.2CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
OpenEye OEToolkits 1.7.2CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(O)=O
ACDLabs 12.01O=C(O)c1ccccc1C(=O)CCC(=O)NCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4OP(=O)(O)O
FormulaC32 H45 N8 O20 P3
Nameo-succinylbenzoyl-N-coenzyme A
ChEMBL
DrugBank
ZINCZINC000198511424
PDB chain5x8f Chain D Residue 501 [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]
PDB5x8f Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode
Resolution1.763 Å
Binding residue
(original residue number in PDB)		K86 P193 H196 I197 S198 F219 A238 L261 G263 G287 M288 S293 Q294 S389 G390 G391 E392 K421 W422 K451 Y452
Binding residue
(residue number reindexed from 1)		K85 P192 H195 I196 S197 F218 A237 L260 G262 G286 M287 S292 Q293 S388 G389 G390 E391 K420 W421 K450 Y451
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T152 S172 H196 T289 E290 I388 N393 K471
Catalytic site (residue number reindexed from 1) T151 S171 H195 T288 E289 I387 N392 K470
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:0016405 CoA-ligase activity
GO:0016874 ligase activity
Biological Process
GO:0009234 menaquinone biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5x8f, PDBe:5x8f, PDBj:5x8f
PDBsum5x8f
PubMed28559280
UniProtP23971|MENE_BACSU 2-succinylbenzoate--CoA ligase (Gene Name=menE)

[Back to BioLiP]