Structure of PDB 3t3h Chain A Binding Site BS01

Receptor Information
>3t3h 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 IDGPV
InChIInChI=1S/C10H13IN2O7/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
InChIKeyNKQVRMXGIOZKRJ-XSEHCYKFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)O)O)I
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)I
ACDLabs 12.01IC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)C2O)CO
CACTVS 3.370OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(I)C(=O)NC2=O
CACTVS 3.370OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(I)C(=O)NC2=O
FormulaC10 H13 I N2 O7
Name1-(beta-D-glucopyranosyl)-5-iodopyrimidine-2,4(1H,3H)-dione;
1-(beta-D-glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione;
1-(D-glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione;
1-(glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL2040853
DrugBank
ZINCZINC000084671507
PDB chain3t3h 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]
PDB3t3h 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
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 N284 D339 H377 T378 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D263 N264 D310 H348 T349 N455 E643 A644 S645 G646
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.71,Ki=1.94uM
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:3t3h, PDBe:3t3h, PDBj:3t3h
PDBsum3t3h
PubMed22267166
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]