Structure of PDB 2amv Chain A Binding Site BS02

Receptor Information
>2amv Chain A (length=829) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDH
LVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEAT
YQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYE
FGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQG
AKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGY
IQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFK
SSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWD
KAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLN
RVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEI
LKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYI
SDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSL
FDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPG
YHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADL
SEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFG
MRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIV
NMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFS
SDRTIAQYAREIWGVEPSRQRLPAPDEKI
Ligand information
Ligand IDBIN
InChIInChI=1S/C20H20ClNO6/c1-5-22-11(4)14(20(27)28-10(2)3)15(12-8-6-7-9-13(12)21)16(18(23)24)17(22)19(25)26/h6-10H,5H2,1-4H3,(H-,23,24,25,26)/p+1
InChIKeyHMSIYRVIPQHZBI-UHFFFAOYSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC[n+]1c(c(c(c(c1C(=O)O)C(=O)O)c2ccccc2Cl)C(=O)OC(C)C)C
CACTVS 3.341CC[n+]1c(C)c(C(=O)OC(C)C)c(c2ccccc2Cl)c(C(O)=O)c1C(O)=O
ACDLabs 10.04O=C(OC(C)C)c1c(c(c([n+](c1C)CC)C(=O)O)C(=O)O)c2ccccc2Cl
FormulaC20 H21 Cl N O6
Name2,3-DICARBOXY-4-(2-CHLORO-PHENYL)-1-ETHYL-5-ISOPROPOXYCARBONYL-6-METHYL-PYRIDINIUM
ChEMBL
DrugBankDB04055
ZINCZINC000003870716
PDB chain2amv Chain A Residue 930 [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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PDB2amv The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I68 Q71 Q72 Y75 R193 E195 F196 R309 R310
Binding residue
(residue number reindexed from 1)		I56 Q59 Q60 Y63 R181 E183 F184 R297 R298
Annotation score1
Binding affinityMOAD: Ki=1.6nM
PDBbind-CN: -logKd/Ki=8.80,Ki=1.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H365 K556 R557 K562 T664 K668
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0008184 glycogen phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0098723 skeletal muscle myofibril

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2amv, PDBe:2amv, PDBj:2amv
PDBsum2amv
PubMed9384557
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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