Structure of PDB 5kdr Chain B Binding Site BS01

Receptor Information
>5kdr Chain B (length=250) Species: 273036 (Staphylococcus aureus RF122) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IMTKCPKCKKIMYTKELAENLNVCFNCDHHIALTAYKRIEAISDEGSFTE
FDKGMTSANPLDFPSYLEKIEKDQQKTGLKEAVVTGTAQLDGMKFGVAVM
DSRFRMGSMGSVIGEKICRIIDYCTENRLPFILFSASGGARMQEGIISLM
QMGKTSVSLKRHSDAGLLYISYLTHPTTGGVSASFASVGDINLSEPKALI
GFAGRRVIEQTINDFQTAEFLLEHGQLDKVVHRNDMRQTLSEILKIHQEV
Ligand information
Ligand IDYT5
InChIInChI=1S/C25H31N3O5/c1-5-6-8-13-19(29)26-18(17-11-9-7-10-12-17)14-20(30)27-22(15(2)3)23(31)21-16(4)24(32)28-25(21)33/h5-13,15-16,18,21-22H,14H2,1-4H3,(H,26,29)(H,27,30)(H,28,32,33)/b6-5+,13-8+/t16-,18-,21+,22-/m0/s1
InChIKeyWMLLJSBRSSYYPT-PQUJRENYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC=CC=CC(=O)N[CH](CC(=O)N[CH](C(C)C)C(=O)[CH]1[CH](C)C(=O)NC1=O)c2ccccc2
CACTVS 3.385C/C=C/C=C/C(=O)N[C@@H](CC(=O)N[C@@H](C(C)C)C(=O)[C@H]1[C@H](C)C(=O)NC1=O)c2ccccc2
OpenEye OEToolkits 2.0.5CC=CC=CC(=O)NC(CC(=O)NC(C(C)C)C(=O)C1C(C(=O)NC1=O)C)c2ccccc2
OpenEye OEToolkits 2.0.5C/C=C/C=C/C(=O)N[C@@H](CC(=O)N[C@@H](C(C)C)C(=O)[C@H]1[C@@H](C(=O)NC1=O)C)c2ccccc2
FormulaC25 H31 N3 O5
NameMoiramide B;
(2~{E},4~{E})-~{N}-[(1~{S})-3-[[(2~{S})-3-methyl-1-[(3~{R},4~{S})-4-methyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-1-oxi danylidene-butan-2-yl]amino]-3-oxidanylidene-1-phenyl-propyl]hexa-2,4-dienamide
ChEMBLCHEMBL181839
DrugBank
ZINCZINC000100194119
PDB chain5kdr Chain B Residue 301 [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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PDB5kdr Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		M134 G166 G167 T206 G207 G208 A231 G232 V235
Binding residue
(residue number reindexed from 1)		M106 G138 G139 T178 G179 G180 A203 G204 V207
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.30,Ki=5nM
Enzymatic activity
Catalytic site (original residue number in PDB) G207 G208
Catalytic site (residue number reindexed from 1) G179 G180
Enzyme Commision number 2.1.3.15: acetyl-CoA carboxytransferase.
Gene Ontology
Molecular Function
GO:0003989 acetyl-CoA carboxylase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0016743 carboxyl- or carbamoyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006633 fatty acid biosynthetic process
GO:2001295 malonyl-CoA biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0009317 acetyl-CoA carboxylase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5kdr, PDBe:5kdr, PDBj:5kdr
PDBsum5kdr
PubMed27471863
UniProtQ2FXM6|ACCD_STAA8 Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (Gene Name=accD)

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