Structure of PDB 7yk1 Chain C Binding Site BS02

Receptor Information
>7yk1 Chain C (length=306) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGE
DVYIIQSGCGEINDNLMELLIMINACKIASSSRVTAVIPCFPYARQDKKD
KSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAV
LQWIRENIAEWKNCIIVSPDAGGAKRVTSIADRLNVEFALIHKEMVLVGD
VKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSGPAISR
INNAAFEAVVVTNTIPQEDKMKHCTKIQVIDISMILAEAIRRTHNGESVS
YLFSHV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-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)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[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)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain7yk1 Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7yk1 Structural basis of human PRPS2 filaments.
Resolution3.08 Å
Binding residue
(original residue number in PDB)		K100 D101 K102 S103 R104
Binding residue
(residue number reindexed from 1)		K99 D100 K101 S102 R103
Annotation score4
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:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process
GO:0006098 pentose-phosphate shunt
GO:0006139 nucleobase-containing compound metabolic process
GO:0006164 purine nucleotide biosynthetic process
GO:0009156 ribonucleoside monophosphate biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0044249 cellular biosynthetic process
Cellular Component
GO:0002189 ribose phosphate diphosphokinase complex
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7yk1, PDBe:7yk1, PDBj:7yk1
PDBsum7yk1
PubMed37248548
UniProtP11908|PRPS2_HUMAN Ribose-phosphate pyrophosphokinase 2 (Gene Name=PRPS2)

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