Structure of PDB 4xrn Chain B Binding Site BS01

Receptor Information
>4xrn Chain B (length=103) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQRQFARVKLPARIRYIGANREGVDARLLDLSAGGFAFTASGAPIQPGDL
YKGKLLFQVDSISFSLEVEFQVRSVDPASRRVGCEFQNLKPREVAALRYL
ITS
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 chain4xrn Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xrn Pilz domain with c-di-gmp of a protein from Pseudomonas aeruginosa
Resolution2.0 Å
Binding residue
(original residue number in PDB)
R6 Q7 R10 D33 L34 S35 G37 G38 F39 R76 R84 C87 E88
Binding residue
(residue number reindexed from 1)
R3 Q4 R7 D30 L31 S32 G34 G35 F36 R73 R81 C84 E85
Annotation score1
Enzymatic activity
Enzyme Commision number 2.4.1.33: mannuronan synthase.
Gene Ontology
Molecular Function
GO:0035438 cyclic-di-GMP binding

View graph for
Molecular Function
External links
PDB RCSB:4xrn, PDBe:4xrn, PDBj:4xrn
PDBsum4xrn
PubMed
UniProtQ9HY69|ALG44_PSEAE Mannuronan synthase (Gene Name=alg44)

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