Structure of PDB 1xoi Chain B Binding Site BS04

Receptor Information
>1xoi Chain B (length=804) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQQ
HYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEEL
EEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIRD
GWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVVL
ALPYDTPVPGYMNNTVNTMRLWSARAPYIQAVLDRNLAENISRVLYPNDN
FFEGKELRLKQEYFVVAATLQDIIRRFKASKFGSTRGAATVFDAFPDQVA
IQLNDTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEAL
ERWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEE
GSKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTN
GITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLREL
AKVKQENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVI
TMYNRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDP
MVGSKLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLN
GALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEA
LPELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQ
DKVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPSDLKI
SLSN
Ligand information
Ligand ID288
InChIInChI=1S/C18H24ClN3O3/c19-13-5-6-15-12(9-13)10-16(21-15)18(25)20-11-17(24)22(7-8-23)14-3-1-2-4-14/h5-6,9-10,14,17,21,23-24H,1-4,7-8,11H2,(H,20,25)/t17-/m1/s1
InChIKeyVXABTOCIIZSEPD-QGZVFWFLSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc1cc2c(cc1)nc(c2)C(=O)NCC(O)N(C3CCCC3)CCO
CACTVS 3.341OCCN([CH](O)CNC(=O)c1[nH]c2ccc(Cl)cc2c1)C3CCCC3
CACTVS 3.341OCCN([C@H](O)CNC(=O)c1[nH]c2ccc(Cl)cc2c1)C3CCCC3
OpenEye OEToolkits 1.5.0c1cc2c(cc1Cl)cc([nH]2)C(=O)NCC(N(CCO)C3CCCC3)O
FormulaC18 H24 Cl N3 O3
Name5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID{[CYCLOPENTYL-(2-HYDROXY-ETHYL)-CARBAMOYL]-METHYL}-AMIDE
ChEMBL
DrugBankDB03288
ZINCZINC000053683779
PDB chain1xoi Chain B Residue 1862 [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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PDB1xoi 5-Chloroindoloyl glycine amide inhibitors of glycogen phosphorylase: synthesis, in vitro, in vivo, and X-ray crystallographic characterization.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R1060 V1064 W1067 P1188 E1190 K1191 S1192 P1229
Binding residue
(residue number reindexed from 1)		R38 V42 W45 P166 E168 K169 S170 P207
Annotation score1
Binding affinityMOAD: ic50=0.057uM
Enzymatic activity
Catalytic site (original residue number in PDB) H1377 K1568 R1569 K1574 T1676 K1680
Catalytic site (residue number reindexed from 1) H343 K534 R535 K540 T642 K646
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:1xoi, PDBe:1xoi, PDBj:1xoi
PDBsum1xoi
PubMed15603973
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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