Structure of PDB 5ks7 Chain A Binding Site BS01

Receptor Information
>5ks7 Chain A (length=123) Species: 1639 (Listeria monocytogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVTQVAQIMNTNPVSITADKSLQAAITVMKEKRVDTLLVVDEGNVLKGFI
DVEQIDLNRRTATSVMDIIEKNVFYVYEDTLLRDTVQRILKRGYKYIPVV
DKDKRLVGIVTRASLVDIVYDSI
Ligand information
Ligand ID2BA
InChIInChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyPDXMFTWFFKBFIN-XPWFQUROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@](=O)(O[C@@H]5[C@@H](CO[P@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6ncnc7N)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P@](O)(=O)O[C@H]4[C@H]3O)n6cnc7c(N)ncnc67
ACDLabs 10.04O=P5(OCC7OC(n1c2ncnc(N)c2nc1)C(O)C7OP(=O)(O)OCC6OC(n3c4ncnc(N)c4nc3)C(O)C6O5)O
FormulaC20 H24 N10 O12 P2
Name(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide;
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate
ChEMBLCHEMBL1229884
DrugBank
ZINCZINC000058661162
PDB chain5ks7 Chain B Residue 500 [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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PDB5ks7 Cyclic di-AMP targets the cystathionine beta-synthase domain of the osmolyte transporter OpuC.
Resolution2.9 Å
Binding residue
(original residue number in PDB)
P259 V260 V280 D281 T282 Y342 T357 R358 A359
Binding residue
(residue number reindexed from 1)
P13 V14 V34 D35 T36 Y96 T111 R112 A113
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.32,Kd=4.8uM
Enzymatic activity
Enzyme Commision number 7.6.2.9: ABC-type quaternary amine transporter.
External links
PDB RCSB:5ks7, PDBe:5ks7, PDBj:5ks7
PDBsum5ks7
PubMed27378384
UniProtQ9KHT9|OPUCA_LISMN Carnitine transport ATP-binding protein OpuCA (Gene Name=opuCA)

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