Structure of PDB 3rl3 Chain A Binding Site BS06

Receptor Information
>3rl3 Chain A (length=276) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTITVDEYSSNPTQAFTHYNINQSRFQPPHVHMVDPIPYDTPKPAGHTRF
VCISDTHSRTDGIQMPYGDILLHTGDFTELGLPSEVKKFNDWLGNLPYEY
KIVIAGNHELTFDKEFMADLVRFPSVSKLKPEDFDNVQSLLTNSIYLQDS
EVTVKGFRIYGAPWTPWFNGWGFNLPRGQSLLDKWNLIPEGTDILMTHGP
PLGFRDWVPKELQRVGCVELLNTVQRRVRPKLHVFGGIHEGYGTMTDGYT
TYINASTCTVSFQPTNPPIIFDLPNP
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain3rl3 Chain A Residue 951 [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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PDB3rl3 Unique utilization of a phosphoprotein phosphatase fold by a mammalian phosphodiesterase associated with WAGR syndrome.
Resolution1.42 Å
Binding residue
(original residue number in PDB)		H67 D86 N117 H118 F183 K225 I253 H254 E255
Binding residue
(residue number reindexed from 1)		H57 D76 N107 H108 F168 K210 I238 H239 E240
Annotation score4
Binding affinityMOAD: ic50=67nM
PDBbind-CN: -logKd/Ki=7.17,IC50=67nM
Enzymatic activity
Enzyme Commision number 3.1.-.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008081 phosphoric diester hydrolase activity
GO:0016208 AMP binding
GO:0016787 hydrolase activity
GO:0019002 GMP binding
GO:0030145 manganese ion binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:3rl3, PDBe:3rl3, PDBj:3rl3
PDBsum3rl3
PubMed21824479
UniProtB1WBP0|MPPD2_RAT Metallophosphoesterase MPPED2 (Gene Name=Mpped2)

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