Structure of PDB 3t3d Chain A Binding Site BS01

Receptor Information
>3t3d 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 IDCJB
InChIInChI=1S/C10H14N2O7/c13-3-4-6(15)7(16)8(17)9(19-4)12-2-1-5(14)11-10(12)18/h1-2,4,6-9,13,15-17H,3H2,(H,11,14,18)/t4-,6-,7+,8-,9-/m1/s1
InChIKeyPBGBADORVLQASN-DDIGBBAMSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)O)O
CACTVS 3.370OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
ACDLabs 12.01O=C1NC(=O)N(C=C1)C2OC(C(O)C(O)C2O)CO
FormulaC10 H14 N2 O7
Name1-beta-D-glucopyranosylpyrimidine-2,4(1H,3H)-dione;
1-D-glucopyranosyl-uracil;
1-beta-D-glucosylpyrimidine-2,4(1H,3H)-dione;
1-D-glucosylpyrimidine-2,4(1H,3H)-dione;
1-glucosylpyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL1096135
DrugBank
ZINCZINC000033976689
PDB chain3t3d 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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PDB3t3d 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
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 N284 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D266 N267 H351 N458 E646 S648 G649
Annotation score1
Binding affinityMOAD: Ki=12.39uM
PDBbind-CN: -logKd/Ki=4.91,Ki=12.39uM
BindingDB: Ki=6100nM
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:3t3d, PDBe:3t3d, PDBj:3t3d
PDBsum3t3d
PubMed22267166
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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