Structure of PDB 3sym Chain A Binding Site BS01

Receptor Information
>3sym Chain A (length=807) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRD
HLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEA
TYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRY
EFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQ
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDGYIQAVLDRN
LAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNFDAF
PDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTV
LPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMS
LVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKF
QNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEA
FIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLN
CLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDV
VNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNM
KFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQ
EYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEE
YVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEP
SRQRLPA
Ligand information
Ligand IDGP0
InChIInChI=1S/C11H15FN2O8/c12-4-1-14(10(20)13-8(4)19)9-7(18)11(21,3-16)6(17)5(2-15)22-9/h1,5-7,9,15-18,21H,2-3H2,(H,13,19,20)/t5-,6-,7+,9-,11+/m1/s1
InChIKeyASRLDHHNHXDEKP-RZBPYSQRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)(CO)O)O)F
OpenEye OEToolkits 1.7.2C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@]([C@@H]([C@H](O2)CO)O)(CO)O)O)F
CACTVS 3.370OC[CH]1O[CH]([CH](O)[C](O)(CO)[CH]1O)N2C=C(F)C(=O)NC2=O
ACDLabs 12.01FC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)(C2O)CO)CO
CACTVS 3.370OC[C@H]1O[C@H]([C@H](O)[C@](O)(CO)[C@@H]1O)N2C=C(F)C(=O)NC2=O
FormulaC11 H15 F N2 O8
Name5-fluoro-1-[3-C-(hydroxymethyl)-beta-D-glucopyranosyl]pyrimidine-2,4(1H,3H)-dione;
5-fluoro-1-[3-C-(hydroxymethyl)-beta-D-glucosyl]pyrimidine-2,4(1H,3H)-dione;
5-fluoro-1-[3-C-(hydroxymethyl)-D-glucosyl]pyrimidine-2,4(1H,3H)-dione;
5-fluoro-1-[3-C-(hydroxymethyl)-glucosyl]pyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000095920630
PDB chain3sym Chain A Residue 843 [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]
PDB3sym 3'-Axial CH(2) OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 N284 H377 T378 N484 E672 S674 G675 X680
Binding residue
(residue number reindexed from 1)		G124 L125 D263 N264 H348 T349 N455 E643 S645 G646 X651
Annotation score1
Binding affinityMOAD: Ki=27.1uM
PDBbind-CN: -logKd/Ki=4.57,Ki=27.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H348 K539 R540 K545 T647 K651
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:3sym, PDBe:3sym, PDBj:3sym
PDBsum3sym
PubMed22296957
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]