Structure of PDB 1em6 Chain B Binding Site BS01

Receptor Information
>1em6 Chain B (length=787) 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
LALPYDTPVPGYMNNTVNTMRLWSARAPGDYIQAVLDRNLAENISRVLYP
NDNFFEGKELRLKQEYFVVAATLQDIIRRFKASTVFDAFPDQVAIQLNDT
HPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERWPVD
LVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSKRIN
MAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGITPRR
WLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVKQE
NKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYNRI
KKDPFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGSKLKVI
FLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGALTIGTMD
GANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPELKLVID
QIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKVSQLYMN
PKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPS
Ligand information
Ligand IDCP4
InChIInChI=1S/C24H24Cl2N4O4/c25-17-1-3-19-15(11-17)13-21(29-19)23(31)27-5-7-33-9-10-34-8-6-28-24(32)22-14-16-12-18(26)2-4-20(16)30-22/h1-4,11-14,29-30H,5-10H2,(H,27,31)(H,28,32)
InChIKeyMWWXABBBAPKJDX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc2c(cc1Cl)cc([nH]2)C(=O)NCCOCCOCCNC(=O)c3cc4cc(ccc4[nH]3)Cl
ACDLabs 10.04Clc1cc2cc(nc2cc1)C(=O)NCCOCCOCCNC(=O)c4cc3cc(Cl)ccc3n4
CACTVS 3.341Clc1ccc2[nH]c(cc2c1)C(=O)NCCOCCOCCNC(=O)c3[nH]c4ccc(Cl)cc4c3
FormulaC24 H24 Cl2 N4 O4
NameBIS[5-CHLORO-1H-INDOL-2-YL-CARBONYL-AMINOETHYL]-ETHYLENE GLYCOL;
CP-526423;
1,2-BIS(2-(5-CHLOROINDOLE-2-CARBONYLAMINO)ETHOXY)ETHANE
ChEMBLCHEMBL434025
DrugBankDB02089
ZINCZINC000012501572
PDB chain1em6 Chain A Residue 862 [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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PDB1em6 Human liver glycogen phosphorylase inhibitors bind at a new allosteric site.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		T38 V40 R60 W67 E190 K191 P229
Binding residue
(residue number reindexed from 1)		T17 V19 R39 W46 E169 K170 P208
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.22,IC50=6nM
BindingDB: IC50=6.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H337 K528 R529 K534 T633 K637
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
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Cellular Component
External links
PDB RCSB:1em6, PDBe:1em6, PDBj:1em6
PDBsum1em6
PubMed10980448
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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