Structure of PDB 3t3e Chain A Binding Site BS01

Receptor Information
>3t3e Chain A (length=810) 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
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNF
DAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTN
HTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLR
RMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEP
HKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVD
DEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQ
LLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAI
GDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGT
GNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGY
NAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFAD
YEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWG
VEPSRQRLPA
Ligand information
Ligand IDGPQ
InChIInChI=1S/C10H13ClN2O7/c11-3-1-13(10(19)12-8(3)18)9-7(17)6(16)5(15)4(2-14)20-9/h1,4-7,9,14-17H,2H2,(H,12,18,19)/t4-,5-,6+,7-,9-/m1/s1
InChIKeyNONSBAHWXCNSII-XSEHCYKFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(Cl)C(=O)NC2=O
ACDLabs 12.01ClC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)C2O)CO
OpenEye OEToolkits 1.7.2C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)O)O)Cl
CACTVS 3.370OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(Cl)C(=O)NC2=O
OpenEye OEToolkits 1.7.2C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)Cl
FormulaC10 H13 Cl N2 O7
Name5-chloro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione;
5-chloro-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione;
5-chloro-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione;
5-chloro-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL2041081
DrugBank
ZINCZINC000084704255
PDB chain3t3e 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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PDB3t3e The sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides towards Glycogen Phosphorylase  b
Resolution2.15 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 H351 T352 N458 E646 A647 S648 G649
Annotation score1
Binding affinityMOAD: Ki=1.02uM
PDBbind-CN: -logKd/Ki=5.99,Ki=1.02uM
BindingDB: Ki=1020nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H351 K542 R543 K548 T650 K654
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:3t3e, PDBe:3t3e, PDBj:3t3e
PDBsum3t3e
PubMed22267166
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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