Structure of PDB 3l7b Chain A Binding Site BS01

Receptor Information
>3l7b Chain A (length=809) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGYIQAVL
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSNFD
AFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNH
TVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRR
MSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPH
KFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDD
EAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQL
LNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIG
DVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTG
NMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYN
AQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADY
EEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGV
EPSRQRLPA
Ligand information
Ligand IDDKZ
InChIInChI=1S/C10H14FN3O5/c11-6-7(16)4(3-15)19-9(8(6)17)14-2-1-5(12)13-10(14)18/h1-2,4,6-9,15-17H,3H2,(H2,12,13,18)/t4-,6+,7-,8-,9-/m1/s1
InChIKeyAGFREDUIXIMAKC-PMPOVCSBSA-N
SMILES
SoftwareSMILES
CACTVS 3.352NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH](F)[CH]2O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)N=C1N)C2C(C(C(C(O2)CO)O)F)O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)F)O
CACTVS 3.352NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H](F)[C@H]2O
FormulaC10 H14 F N3 O5
Name4-amino-1-(3-deoxy-3-fluoro-beta-D-glucopyranosyl)pyrimidin-2(1H)-one;
4-amino-1-(3-deoxy-3-fluoro-beta-D-glucosyl)pyrimidin-2(1H)-one;
4-amino-1-(3-deoxy-3-fluoro-D-glucosyl)pyrimidin-2(1H)-one;
4-amino-1-(3-deoxy-3-fluoro-glucosyl)pyrimidin-2(1H)-one
ChEMBL
DrugBank
ZINCZINC000049070576
PDB chain3l7b 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

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PDB3l7b 1-(3-Deoxy-3-fluoro-beta-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G135 L136 N284 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N267 H350 N457 E645 S647 G648
Annotation score1
Binding affinityMOAD: Ki=4.01mM
PDBbind-CN: -logKd/Ki=2.40,Ki=4.01mM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H350 K541 R542 K547 T649 K653
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:3l7b, PDBe:3l7b, PDBj:3l7b
PDBsum3l7b
PubMed20430629
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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