Structure of PDB 2qn3 Chain A Binding Site BS01

Receptor Information
>2qn3 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 IDF55
InChIInChI=1S/C14H17ClN2O7/c15-7-3-1-6(2-4-7)12(22)16-14(23)17-13-11(21)10(20)9(19)8(5-18)24-13/h1-4,8-11,13,18-21H,5H2,(H2,16,17,22,23)/t8-,9-,10+,11-,13-/m1/s1
InChIKeyYTUMHTAWGXUOIS-BZNQNGANSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NC(=O)NC2C(C(C(C(O2)CO)O)O)O)Cl
CACTVS 3.341OC[C@H]1O[C@@H](NC(=O)NC(=O)c2ccc(Cl)cc2)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04O=C(NC1OC(C(O)C(O)C1O)CO)NC(=O)c2ccc(Cl)cc2
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NC(=O)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)Cl
CACTVS 3.341OC[CH]1O[CH](NC(=O)NC(=O)c2ccc(Cl)cc2)[CH](O)[CH](O)[CH]1O
FormulaC14 H17 Cl N2 O7
NameN-{[(4-chlorophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine;
N-{[(4-chlorophenyl)carbonyl]carbamoyl}-beta-D-glucosylamine;
N-{[(4-chlorophenyl)carbonyl]carbamoyl}-D-glucosylamine;
N-{[(4-chlorophenyl)carbonyl]carbamoyl}-glucosylamine
ChEMBLCHEMBL1232636
DrugBank
ZINCZINC000038965467
PDB chain2qn3 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

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PDB2qn3 N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation
Resolution1.96 Å
Binding residue
(original residue number in PDB)		G135 L136 N282 D283 H377 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N268 D269 H354 N461 E649 A650 S651 G652
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.36,Ki=4.4uM
BindingDB: Ki=4400nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2qn3, PDBe:2qn3, PDBj:2qn3
PDBsum2qn3
PubMed
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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