Structure of PDB 2ydc Chain A Binding Site BS01

Receptor Information
>2ydc Chain A (length=217) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDFLPLYFGWFLTKKSSETLRKAGQVFLEELGNHKAFKKELRHFISGDEP
KEKLELVSYFGKRPPGVLHCTTKFCDYGKAAGAEEYAQQEVVKRSYGKAF
KLSISALFVTPKTAGAQVVLTDQELQLWPSDLDKPSASEGLPPGSRAHVT
LGCAADVQPVQTGLDLLDILQQVKGGSQGEAVGELPRGKLYSLGKGRWML
SLTKKMEVKAIFTGYYG
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain2ydc Chain A Residue 1379 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ydc Structural Characterization of Mouse Cnpase Complexed with Active-Site Ligands
Resolution2.05 Å
Binding residue
(original residue number in PDB)		H230 T232 F235 H309 T311 P320 V321
Binding residue
(residue number reindexed from 1)		H69 T71 F74 H148 T150 P159 V160
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.37: 2',3'-cyclic-nucleotide 3'-phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
Biological Process
GO:0009214 cyclic nucleotide catabolic process
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ydc, PDBe:2ydc, PDBj:2ydc
PDBsum2ydc
PubMed
UniProtP16330|CN37_MOUSE 2',3'-cyclic-nucleotide 3'-phosphodiesterase (Gene Name=Cnp)

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