Structure of PDB 1l7x Chain B Binding Site BS05

Receptor Information
>1l7x Chain B (length=795) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVENVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIR
TQQHYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDI
EELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQK
IRDGWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQ
VVLALPYDTPVPGYMNNTVNTMRLWSARAPNDGDYIQAVLDRNLAENISR
VLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFVFDAFPDQVAI
QLNDTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALE
RWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEG
SKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNG
ITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELA
KVKQENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVIT
MYNRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPM
VGSKLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNG
ALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEAL
PELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQD
KVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPS
Ligand information
Ligand IDCFF
InChIInChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
InChIKeyRYYVLZVUVIJVGH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cn1cnc2N(C)C(=O)N(C)C(=O)c12
ACDLabs 10.04O=C2N(c1ncn(c1C(=O)N2C)C)C
OpenEye OEToolkits 1.5.0Cn1cnc2c1C(=O)N(C(=O)N2C)C
FormulaC8 H10 N4 O2
NameCAFFEINE;
3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE
ChEMBLCHEMBL113
DrugBankDB00201
ZINCZINC000000001084
PDB chain1l7x Chain B Residue 1863 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1l7x Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F285 H571 A610 G612 Y613
Binding residue
(residue number reindexed from 1)		F258 H536 A575 G577 Y578
Annotation score1
Binding affinityMOAD: Kd=92uM
PDBbind-CN: -logKd/Ki=4.04,Kd=92uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H342 K533 R534 K539 T641 K645
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002060 purine nucleobase binding
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005536 D-glucose binding
GO:0008184 glycogen phosphorylase activity
GO:0016208 AMP binding
GO:0016757 glycosyltransferase activity
GO:0019842 vitamin binding
GO:0030170 pyridoxal phosphate binding
GO:0030246 carbohydrate binding
GO:0032052 bile acid binding
GO:0042802 identical protein binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process
GO:0009617 response to bacterium
GO:0042593 glucose homeostasis
GO:0070266 necroptotic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1l7x, PDBe:1l7x, PDBj:1l7x
PDBsum1l7x
PubMed12204691
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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