Structure of PDB 5xge Chain A Binding Site BS01

Receptor Information
>5xge Chain A (length=548) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DAERERAQITLASIGDGVITADTQGGISYLNPAAEQMTNWTLDKARGLPL
ASLFRIVDLIEQILSGEIDGGREHSKLVLRHDGSSVPVTLVGAPIHRGAE
ITGVVLVLHDMTRERQYMARLSWQATHDALTGLTNRREFEYRLQIALERL
ERNSGRHALMFLDLDQFKLVNDTCGHAAGDELLRQVCTLLQQGLREGDTL
ARLGGDEFGILLENCPAEKAVEIADHLRKTIQDLHFTWSGQPFNCTVSVG
LVHLLPGISTLEEALRSADMACYMAKEKGRNRVQVFHQDDVELSMRFGEM
TWVQRIHLALEEDRFSLYAQPIVPLGEGAEEGLHVELLLRLRDEGGRLVP
PLSFIPAAERYGLMTLIDRWVVENAFRTLVERAQDPRAEPIGTCAINLSG
ATIGDESFLQFLTELFARYRIPPQTICFEVTETVAVANLASAIRFINELK
DTGCRFSLDDFCAGMSSFIYLKHLPVDYLKIDGSFVKDMLEDPIDRAMVQ
VINHIGHVMGKRTIAEFVETVEVMEALREIGIDYAQGLAIGAPLPFSR
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 chain5xge Chain A Residue 901 [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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PDB5xge Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa.
Resolution3.31 Å
Binding residue
(original residue number in PDB)
Q569 L587 L588 R589 D617 N646 F766 E768 G786 L787
Binding residue
(residue number reindexed from 1)
Q320 L338 L339 R340 D368 N397 F517 E519 G537 L538
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0006355 regulation of DNA-templated transcription

View graph for
Biological Process
External links
PDB RCSB:5xge, PDBe:5xge, PDBj:5xge
PDBsum5xge
PubMed29109186
UniProtQ9I580

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