Structure of PDB 3cej Chain B Binding Site BS04

Receptor Information
>3cej Chain B (length=790) 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
ALPYDTPVPGYMNNTVNTMRLWSARAPDYIQAVLDRNLAENISRVLYPND
NFFEGKELRLKQEYFVVAATLQDIIRRFKASKFVFDAFPDQVAIQLNDTH
PALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERWPVDL
VEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSKRINM
AHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGITPRRW
LLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVKQEN
KLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYNRIK
KDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGSKLK
VIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGALTIGT
MDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPELKLV
IDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKVSQLY
MNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPSD
Ligand information
Ligand IDAVF
InChIInChI=1S/C20H17ClF3N3O4/c21-13-9-15(24)14(23)8-12(13)18(28)26-20(31)25-16-7-11(22)1-2-17(16)27-5-3-10(4-6-27)19(29)30/h1-2,7-10H,3-6H2,(H,29,30)(H2,25,26,28,31)
InChIKeyKAJJGOCSAXKXBD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Fc1cc(c(Cl)cc1F)C(=O)NC(=O)Nc2cc(F)ccc2N3CCC(C(=O)O)CC3
CACTVS 3.341OC(=O)C1CCN(CC1)c2ccc(F)cc2NC(=O)NC(=O)c3cc(F)c(F)cc3Cl
OpenEye OEToolkits 1.5.0c1cc(c(cc1F)NC(=O)NC(=O)c2cc(c(cc2Cl)F)F)N3CCC(CC3)C(=O)O
FormulaC20 H17 Cl F3 N3 O4
Name1-{2-[3-(2-Chloro-4,5-difluoro-benzoyl)-ureido]-4-fluoro-phenyl}-piperidine-4-carboxylic acid;
1-[2-({[(2-chloro-4,5-difluorophenyl)carbonyl]carbamoyl}amino)-4-fluorophenyl]piperidine-4-carboxylic acid
ChEMBLCHEMBL1231099
DrugBankDB07396
ZINCZINC000053683030
PDB chain3cej Chain B Residue 833 [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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PDB3cej Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		W67 I68 Q71 Q72 Y75 K191 R193 F196 R310
Binding residue
(residue number reindexed from 1)		W45 I46 Q49 Q50 Y53 K169 R171 F174 R277
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H336 K527 R528 K533 T635 K639
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:3cej, PDBe:3cej, PDBj:3cej
PDBsum3cej
PubMed18373353
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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