Structure of PDB 6pfj Chain A Binding Site BS01

Receptor Information
>6pfj Chain A (length=219) Species: 1520455 (Streptomyces sp. PanSC19) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APTSLDELWRSYKETGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQA
DFVSSGVFGLIDAIEKFDVERAIKFETYAITRIRGAMIDELRALDWIPRS
VRQKARNVERAYATLEAQLRRTPSETEVAAEMDISLEDLHAVFSQLSLAN
VVALEELLHRRLLARAINTLPEREKTVVTLYYYEGLTLAEIGHVLGVTES
RVSQIHTKSVLQLRAKLAD
Ligand information
Ligand IDC2E
InChIInChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKeyPKFDLKSEZWEFGL-MHARETSRSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C7NC(=Nc1c7ncn1C6OC5COP(=O)(OC4C(OC(n2c3N=C(N)NC(=O)c3nc2)C4O)COP(=O)(O)OC5C6O)O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[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)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[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(=O)NC(=Nc67)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[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(=O)NC(=Nc67)N
FormulaC20 H24 N10 O14 P2
Name9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one);
c-di-GMP;
Cyclic diguanosine monophosphate
ChEMBLCHEMBL1231573
DrugBank
ZINCZINC000072319544
PDB chain6pfj Chain T Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6pfj c-di-GMP Arms an Anti-sigma to Control Progression of Multicellular Differentiation in Streptomyces.
Resolution2.08 Å
Binding residue
(original residue number in PDB)
G61 R62 V65
Binding residue
(residue number reindexed from 1)
G37 R38 V41
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.41,Kd=0.39uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016987 sigma factor activity
Biological Process
GO:0006352 DNA-templated transcription initiation
GO:0006355 regulation of DNA-templated transcription
GO:2000142 regulation of DNA-templated transcription initiation

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6pfj, PDBe:6pfj, PDBj:6pfj
PDBsum6pfj
PubMed31810759
UniProtA0A3N1Q704

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