Structure of PDB 2zb2 Chain B Binding Site BS04

Receptor Information
>2zb2 Chain B (length=791) 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
LALPYDTPVPGYMNNTVNTMRLWSARAPNGDYIQAVLDRNLAENISRVLY
PNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASTVFDAFPDQVAIQLND
THPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERWPV
DLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSKRI
NMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGITPR
RWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVKQ
ENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYNR
IKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGSK
LKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGALTI
GTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPELK
LVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKVSQ
LYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPS
Ligand information
Ligand IDA46
InChIInChI=1S/C17H15ClN2O3/c18-12-3-6-14-11(7-12)8-15(20-14)17(23)19-13-4-1-10(2-5-13)16(22)9-21/h1-8,16,20-22H,9H2,(H,19,23)/t16-/m0/s1
InChIKeySHCHFGSUYJUEBR-INIZCTEOSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@H](O)c1ccc(NC(=O)c2[nH]c3ccc(Cl)cc3c2)cc1
CACTVS 3.341OC[CH](O)c1ccc(NC(=O)c2[nH]c3ccc(Cl)cc3c2)cc1
OpenEye OEToolkits 1.5.0c1cc(ccc1[C@H](CO)O)NC(=O)c2cc3cc(ccc3[nH]2)Cl
ACDLabs 10.04Clc1cc2c(cc1)nc(c2)C(=O)Nc3ccc(cc3)C(O)CO
OpenEye OEToolkits 1.5.0c1cc(ccc1C(CO)O)NC(=O)c2cc3cc(ccc3[nH]2)Cl
FormulaC17 H15 Cl N2 O3
Name5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide
ChEMBL
DrugBankDB07315
ZINCZINC000013975043
PDB chain2zb2 Chain B Residue 850 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2zb2 Synthesis of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives as inhibitors of human liver glycogen phosphorylase a.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		R60 W67 P188 E190 K191 P229
Binding residue
(residue number reindexed from 1)		R39 W46 P167 E169 K170 P208
Annotation score1
Binding affinityMOAD: ic50=0.9uM
BindingDB: IC50=900nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H338 K529 R530 K535 T637 K641
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2zb2, PDBe:2zb2, PDBj:2zb2
PDBsum2zb2
PubMed18434170
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

[Back to BioLiP]