Structure of PDB 3l7c Chain A Binding Site BS01

Receptor Information
>3l7c 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]
QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRD
HLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEA
TYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRY
EFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQ
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGYIQAVL
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKRT
NFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAY
TNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDR
LRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYEL
EPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSY
VDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYK
RQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLIT
AIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEAS
GTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQR
GYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVF
ADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREI
WGVEPSRQRLPA
Ligand information
Ligand IDDK4
InChIInChI=1S/C10H12F2N2O6/c11-3-1-14(10(19)13-8(3)18)9-7(17)5(12)6(16)4(2-15)20-9/h1,4-7,9,15-17H,2H2,(H,13,18,19)/t4-,5+,6-,7-,9-/m1/s1
InChIKeyBXHWKGLMPCAUQA-XLKNOJSPSA-N
SMILES
SoftwareSMILES
CACTVS 3.352OC[C@H]1O[C@H]([C@H](O)[C@@H](F)[C@@H]1O)N2C=C(F)C(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)F)O)F
OpenEye OEToolkits 1.7.0C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)F)O)F
CACTVS 3.352OC[CH]1O[CH]([CH](O)[CH](F)[CH]1O)N2C=C(F)C(=O)NC2=O
FormulaC10 H12 F2 N2 O6
Name1-(3-deoxy-3-fluoro-beta-D-glucopyranosyl)-5-fluoropyrimidine-2,4(1H,3H)-dione;
1-(3-deoxy-3-fluoro-beta-D-glucosyl)-5-fluoropyrimidine-2,4(1H,3H)-dione;
1-(3-deoxy-3-fluoro-D-glucosyl)-5-fluoropyrimidine-2,4(1H,3H)-dione;
1-(3-deoxy-3-fluoro-glucosyl)-5-fluoropyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000049111594
PDB chain3l7c 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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PDB3l7c 1-(3-Deoxy-3-fluoro-beta-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 N284 H377 T378 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D266 N267 H353 T354 N460 E648 A649 S650 G651
Annotation score1
Binding affinityMOAD: Ki=3.67mM
PDBbind-CN: -logKd/Ki=2.44,Ki=3.67mM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H353 K544 R545 K550 T652 K656
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:3l7c, PDBe:3l7c, PDBj:3l7c
PDBsum3l7c
PubMed20430629
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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