Structure of PDB 1l5s Chain A Binding Site BS01

Receptor Information
>1l5s Chain A (length=793) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQ
QHYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEE
LEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIR
DGWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVV
LALPYDTPVPGYMNNTVNTMRLWSARAPNDDYIQAVLDRNLAENISRVLY
PNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFVFDAFPDQVAIQLN
DTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERWP
VDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSKR
INMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGITP
RRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVK
QENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYN
RIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGS
KLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGALT
IGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPEL
KLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKVS
QLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPSD
Ligand information
Ligand IDNBG
InChIInChI=1S/C8H15NO6/c1-3(11)9-8-7(14)6(13)5(12)4(2-10)15-8/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8-/m1/s1
InChIKeyIBONACLSSOLHFU-JAJWTYFOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)N[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
CACTVS 3.341CC(=O)N[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
CACTVS 3.341CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04O=C(NC1OC(C(O)C(O)C1O)CO)C
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(C(O1)CO)O)O)O
FormulaC8 H15 N O6
NameN-acetyl-beta-D-glucopyranosylamine;
1-N-ACETYL-BETA-D-GLUCOSAMINE;
N-acetyl-beta-D-glucosylamine;
N-acetyl-D-glucosylamine;
N-acetyl-glucosylamine
ChEMBLCHEMBL335315
DrugBankDB02320
ZINC
PDB chain1l5s Chain A Residue 861 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1l5s Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		N284 H377 T378 V455 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		N254 H339 T340 V417 N446 E634 S636 G637
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H339 K530 R531 K536 T638 K642
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:1l5s, PDBe:1l5s, PDBj:1l5s
PDBsum1l5s
PubMed12204691
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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