Structure of PDB 3lpn Chain B Binding Site BS02

Receptor Information
>3lpn Chain B (length=286) Species: 50339 (Thermoplasma volcanium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNI
FIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGE
PISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYK
NVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVD
VNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENK
ILQNADEIHVTDTVESKFSDISVYQEVCNYIRDIDA
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain3lpn Chain B Residue 287 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lpn The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R91 Q92 H93 Y96 H124 D125
Binding residue
(residue number reindexed from 1)		R91 Q92 H93 Y96 H124 D125
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.6.1: ribose-phosphate diphosphokinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004749 ribose phosphate diphosphokinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process
GO:0006164 purine nucleotide biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0002189 ribose phosphate diphosphokinase complex
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3lpn, PDBe:3lpn, PDBj:3lpn
PDBsum3lpn
PubMed21963988
UniProtQ97CA5|KPRS_THEVO Ribose-phosphate pyrophosphokinase (Gene Name=prs)

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