Structure of PDB 6k6t Chain B Binding Site BS01

Receptor Information
>6k6t 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 IDC2I
InChIInChI=1S/C20H22N8O14P2/c29-11-13-7(39-19(11)27-5-25-9-15(27)21-3-23-17(9)31)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)30)28-6-26-10-16(28)22-4-24-18(10)32/h3-8,11-14,19-20,29-30H,1-2H2,(H,33,34)(H,35,36)(H,21,23,31)(H,22,24,32)/t7-,8+,11-,12-,13-,14-,19+,20+/m0/s1
InChIKeyVFTRASQVWRBMKD-PHSICLOESA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1[CH]2O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O[P](O)(=O)OC[CH]2O[CH]1n4cnc5C(=O)N=CNc45)n6cnc7C(=O)N=CNc67
CACTVS 3.385O[C@H]1[C@H]2O[P](O)(=O)OC[C@@H]3O[C@H]([C@@H](O)[C@H]3O[P](O)(=O)OC[C@H]2O[C@H]1n4cnc5C(=O)N=CNc45)n6cnc7C(=O)N=CNc67
OpenEye OEToolkits 2.0.7c1nc2c(n1[C@H]3[C@H]([C@@H]4[C@H](O3)COP(=O)(O[C@H]5[C@H](COP(=O)(O4)O)O[C@H]([C@H]5O)n6cnc7c6NC=NC7=O)O)O)NC=NC2=O
OpenEye OEToolkits 2.0.7c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6NC=NC7=O)O)O)NC=NC2=O
FormulaC20 H22 N8 O14 P2
Name9-[(1R,6R,8R,9S,10R,15S,17R,18S)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-17-(6-oxidanylidene-3H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-3H-purin-6-one
ChEMBL
DrugBank
ZINC
PDB chain6k6t 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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PDB6k6t Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form
Resolution2.2 Å
Binding residue
(original residue number in PDB)
Q31 L47 V48 R49 A56 N95 M182 G216 E218 G236 Y237
Binding residue
(residue number reindexed from 1)
Q11 L27 V28 R29 A36 N75 M162 G196 E198 G216 Y217
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.1: phosphodiesterase I.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:6k6t, PDBe:6k6t, PDBj:6k6t
PDBsum6k6t
PubMed
UniProtA0A0H3AJ04

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