Structure of PDB 1w25 Chain A Binding Site BS03

Receptor Information
>1w25 Chain A (length=454) Species: 190650 (Caulobacter vibrioides CB15) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIIL
LDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASD
FLTKPIDDVMLFARVRSLTRFKLVIDELRQREASGRRMGVIAGAAARLDG
LGGRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKISAGGPVDLVIV
NAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDI
LSRPIDPQELSARVKTQIQRKRYTDYLRNNLDHSLELAVTDQLTGLHNRR
YMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGHDIGDEVLREFA
LRLASNVRAIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPFT
VAHGREMLNVTISIGVSATAGEGDTPEALLKRADEGVYQAKASGRNAVVG
KAAH
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 chain1w25 Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1w25 Structural Basis of Activity and Allosteric Control of Diguanylate Cyclase
Resolution2.7 Å
Binding residue
(original residue number in PDB)
R178 R359 D362 D383 I387 R390
Binding residue
(residue number reindexed from 1)
R177 R358 D361 D382 I386 R389
Annotation score4
Binding affinityManual survey: Ki=0.5uM (15569936)
PDBbind-CN: -logKd/Ki=6.30,Ki=0.5uM
Enzymatic activity
Enzyme Commision number 2.7.7.65: diguanylate cyclase.
Gene Ontology
Molecular Function
GO:0005525 GTP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0052621 diguanylate cyclase activity
Biological Process
GO:0000160 phosphorelay signal transduction system
GO:0030154 cell differentiation
GO:0043709 cell adhesion involved in single-species biofilm formation
GO:1902201 negative regulation of bacterial-type flagellum-dependent cell motility
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:1w25, PDBe:1w25, PDBj:1w25
PDBsum1w25
PubMed15569936
UniProtB8GZM2|PLED_CAUVN Response regulator PleD (Gene Name=pleD)

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