Structure of PDB 8dbk Chain F Binding Site BS04

Receptor Information
>8dbk Chain F (length=309) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGE
DVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKD
KSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAV
LKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKEDRMVLV
GDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAI
SRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAIRRTHNGES
VSYLFSHVP
Ligand information
Ligand IDHSX
InChIInChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5+/m1/s1
InChIKeyKTVPXOYAKDPRHY-AIHAYLRMSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCC1OC(O)C(O)C1O
CACTVS 3.341O[C@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]1O
FormulaC5 H11 O8 P
Name5-O-phosphono-alpha-D-ribofuranose;
5-O-phosphono-alpha-D-ribose;
5-O-phosphono-D-ribose;
5-O-phosphono-ribose
ChEMBLCHEMBL605020
DrugBank
ZINCZINC000004096190
PDB chain8dbk Chain F Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dbk Human PRPS1 filaments stabilize allosteric sites to regulate activity.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H130 D220 D221 M222 D224 T225 T228
Binding residue
(residue number reindexed from 1)		H129 D212 D213 M214 D216 T217 T220
Annotation score5
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:0006144 purine nucleobase metabolic process
GO:0006164 purine nucleotide biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006796 phosphate-containing compound metabolic process
GO:0007399 nervous system development
GO:0009156 ribonucleoside monophosphate biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0034418 urate biosynthetic process
GO:0044249 cellular biosynthetic process
GO:0046101 hypoxanthine biosynthetic process
GO:0090407 organophosphate 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:8dbk, PDBe:8dbk, PDBj:8dbk
PDBsum8dbk
PubMed36747094
UniProtP60891|PRPS1_HUMAN Ribose-phosphate pyrophosphokinase 1 (Gene Name=PRPS1)

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