Structure of PDB 3amv Chain A Binding Site BS03

Receptor Information
>3amv Chain A (length=812) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFA
LAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLAL
ENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAA
YGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYG
RVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNGGYI
QAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKS
SNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCA
YTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVD
RLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYE
LEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLS
YVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEY
KRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLI
TAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEA
SGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQ
RGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKV
FADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYARE
IWGVEPSRQRLP
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 chain3amv 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

[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]
PDB3amv Allosteric inhibition of glycogen phosphorylase a by the potential antidiabetic drug 3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5,6-tricarbo xylate.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		I68 Q71 Q72 Y75 R193 F196 R242 R309 R310
Binding residue
(residue number reindexed from 1)		I64 Q67 Q68 Y71 R189 F192 R238 R296 R297
Annotation score1
Binding affinityMOAD: Ki=10.8nM
PDBbind-CN: -logKd/Ki=7.97,Ki=10.8nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H354 K545 R546 K551 T653 K657
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3amv, PDBe:3amv, PDBj:3amv
PDBsum3amv
PubMed10548038
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]