Structure of PDB 8dbf Chain C Binding Site BS03
Receptor Information
>8dbf Chain C (length=316) Species:
9606
(Homo sapiens) [
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PNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGE
DVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKD
KSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAV
LKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANE
VDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHG
IFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAIR
RTHNGESVSYLFSHVP
Ligand information
Ligand ID
ADP
InChI
InChI=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
InChIKey
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(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 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Formula
C10 H15 N5 O10 P2
Name
ADENOSINE-5'-DIPHOSPHATE
ChEMBL
CHEMBL14830
DrugBank
DB16833
ZINC
ZINC000012360703
PDB chain
8dbf Chain C Residue 402 [
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Receptor-Ligand Complex Structure
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PDB
8dbf
Human PRPS1 filaments stabilize allosteric sites to regulate activity.
Resolution
2.2 Å
Binding residue
(original residue number in PDB)
D143 Y146 S308 V309 S310 F313
Binding residue
(residue number reindexed from 1)
D142 Y145 S307 V308 S309 F312
Annotation score
4
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:8dbf
,
PDBe:8dbf
,
PDBj:8dbf
PDBsum
8dbf
PubMed
36747094
UniProt
P60891
|PRPS1_HUMAN Ribose-phosphate pyrophosphokinase 1 (Gene Name=PRPS1)
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