Structure of PDB 6ih1 Chain B Binding Site BS01

Receptor Information
>6ih1 Chain B (length=237) Species: 345073 (Vibrio cholerae O395) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLDFDFTMAFQPIVNCRTKEIFGYEALVRGLNNESAYSVISRVNEDNRYL
FDQMCRVKAIALAAKLGLTSKLSINFLPNAIYVPERCIRTTLEAAKRYQF
PIENIMFEFTEAERVEDVNHIKRIVEYYKSLGFQTAIDDFGSGYSGLNLL
ADFQTNIVKVDMGLIRNIHADQVRQSIMKNCLKLFSDLNIQPLAEGVESH
AEFAWLKAAGVELMQGYYFAKPGFESLPSVNPEFSEA
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 chain6ih1 Chain B Residue 501 [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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PDB6ih1 Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication.
Resolution1.95 Å
Binding residue
(original residue number in PDB)
Q31 L47 V48 R49 I60 N95 L97 M182 G216 E218 G236 Y237
Binding residue
(residue number reindexed from 1)
Q11 L27 V28 R29 I40 N75 L77 M162 G196 E198 G216 Y217
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.4.52: cyclic-guanylate-specific phosphodiesterase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:6ih1, PDBe:6ih1, PDBj:6ih1
PDBsum6ih1
PubMed31647518
UniProtA0A0H3AJ04

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