Structure of PDB 3qyy Chain A Binding Site BS01

Receptor Information
>3qyy Chain A (length=153) Species: 340 (Xanthomonas campestris pv. campestris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HALFDPLTEALNRRGCEQAMRDSVTAAQREGWPFVLFVLDMDNLKPINDR
FGHLAGDRVLVRLVESAYGWLGAQDWIGRWGGDEFLIGVHASEDEATLKL
NQWLSMLEREAPLHVSAGSAVCEVGIDATELYRRADAAMYRAKFSGGRRL
VRD
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 chain3qyy Chain A Residue 487 [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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PDB3qyy The structure and inhibition of a GGDEF diguanylate cyclase complexed with (c-di-GMP)(2) at the active site
Resolution1.9 Å
Binding residue
(original residue number in PDB)
L177 K178 N181 H186 G189 D190 R212 G215 D216
Binding residue
(residue number reindexed from 1)
L44 K45 N48 H53 G56 D57 R79 G82 D83
Annotation score4
Binding affinityManual survey: Ki=6.54uM (22120736)
MOAD: Kd=8.26uM
PDBbind-CN: -logKd/Ki=5.08,Kd=8.26uM
Enzymatic activity
Enzyme Commision number 2.7.7.65: diguanylate cyclase.
External links