Structure of PDB 3l7a Chain A Binding Site BS01

Receptor Information
>3l7a Chain A (length=811) 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
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKTN
FDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYT
NHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRL
RRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELE
PHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYV
DDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKR
QLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITA
IGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASG
TGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRG
YNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFA
DYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIW
GVEPSRQRLPA
Ligand information
Ligand IDDKY
InChIInChI=1S/C17H18FN3O6/c18-12-13(23)10(8-22)27-16(14(12)24)21-7-6-11(20-17(21)26)19-15(25)9-4-2-1-3-5-9/h1-7,10,12-14,16,22-24H,8H2,(H,19,20,25,26)/t10-,12+,13-,14-,16-/m1/s1
InChIKeyPUCZITRLESUWFB-PBEGBBSFSA-N
SMILES
SoftwareSMILES
CACTVS 3.352OC[C@H]1O[C@H]([C@H](O)[C@@H](F)[C@@H]1O)N2C=CC(=NC2=O)NC(=O)c3ccccc3
OpenEye OEToolkits 1.7.0c1ccc(cc1)C(=O)NC2=NC(=O)N(C=C2)C3C(C(C(C(O3)CO)O)F)O
OpenEye OEToolkits 1.7.0c1ccc(cc1)C(=O)NC2=NC(=O)N(C=C2)[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)F)O
CACTVS 3.352OC[CH]1O[CH]([CH](O)[CH](F)[CH]1O)N2C=CC(=NC2=O)NC(=O)c3ccccc3
FormulaC17 H18 F N3 O6
Name1-(3-deoxy-3-fluoro-beta-D-glucopyranosyl)-4-[(phenylcarbonyl)amino]pyrimidin-2(1H)-one
ChEMBL
DrugBank
ZINCZINC000049070572
PDB chain3l7a 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]
PDB3l7a 1-(3-Deoxy-3-fluoro-beta-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G135 L136 N282 N284 F285 H377 A383 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N265 N267 F268 H352 A358 N459 E647 A648 S649 G650
Annotation score1
Binding affinityMOAD: Ki=46.42uM
PDBbind-CN: -logKd/Ki=4.33,Ki=46.42uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H352 K543 R544 K549 T651 K655
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:3l7a, PDBe:3l7a, PDBj:3l7a
PDBsum3l7a
PubMed20430629
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]