Structure of PDB 3np7 Chain A Binding Site BS02

Receptor Information
>3np7 Chain A (length=813) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLNVGGYIQ
AVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSS
TNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCA
YTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVD
RLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYE
LEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLS
YVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEY
KRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLI
TAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEA
SGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQ
RGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKV
FADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYARE
IWGVEPSRQRLPA
Ligand information
Ligand IDZ15
InChIInChI=1S/C12H15ClO7/c13-5-2-6(15)4(1-7(5)16)12-11(19)10(18)9(17)8(3-14)20-12/h1-2,8-12,14-19H,3H2/t8-,9-,10+,11-,12+/m1/s1
InChIKeyLHMIFDKRIZSEFV-ZIQFBCGOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1c(c(cc(c1O)Cl)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)c2cc(O)c(Cl)cc2O
CACTVS 3.370OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)c2cc(O)c(Cl)cc2O
ACDLabs 12.01Clc1c(O)cc(c(O)c1)C2OC(CO)C(O)C(O)C2O
OpenEye OEToolkits 1.7.0c1c(c(cc(c1O)Cl)O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
FormulaC12 H15 Cl O7
Name(1S)-1,5-anhydro-1-(4-chloro-2,5-dihydroxyphenyl)-D-glucitol
ChEMBLCHEMBL1738938
DrugBank
ZINCZINC000066156449
PDB chain3np7 Chain A Residue 998 [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]
PDB3np7 Halogen-substituted (C-beta-D-glucopyranosyl)-hydroquinone regioisomers: synthesis, enzymatic evaluation and their binding to glycogen phosphorylase.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 N284 D339 H341 H377 T378 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D269 N270 D316 H318 H354 T355 N461 E649 S651 G652
Annotation score1
Binding affinityMOAD: ic50=95uM
PDBbind-CN: -logKd/Ki=4.02,IC50=95uM
BindingDB: IC50=169900nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H354 K545 R546 K551 T653 K657
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:3np7, PDBe:3np7, PDBj:3np7
PDBsum3np7
PubMed21821421
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]