Structure of PDB 3pjt Chain A Binding Site BS01

Receptor Information
>3pjt Chain A (length=240) Species: 205922 (Pseudomonas fluorescens Pf0-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQT
IPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADP
QALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLS
LQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAH
SIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG
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 chain3pjt Chain A Residue 2256 [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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PDB3pjt Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis.
Resolution2.5154 Å
Binding residue
(original residue number in PDB)
Q431 K446 L448 S449 R450 A461 G462 L465 M481 N499 Q560 R561 R618 E620 G638 Q639
Binding residue
(residue number reindexed from 1)
Q23 K38 L40 S41 R42 A53 G54 L57 M73 N91 Q152 R153 R210 E212 G230 Q231
Annotation score4
Binding affinityManual survey: Kd=13.1uM (21304926)
PDBbind-CN: -logKd/Ki=4.88,Kd=13.1uM
Enzymatic activity
Enzyme Commision number ?
External links