Structure of PDB 1k08 Chain A Binding Site BS01

Receptor Information
>1k08 Chain A (length=817) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDH
LVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEAT
YQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYE
FGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQG
AKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGY
IQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFK
SSKTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVK
TCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPG
DVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKD
FYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRK
LLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRI
HEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMII
KLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAG
TEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDR
LDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDR
FKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQY
AREIWGVEPSRQRLPAP
Ligand information
Ligand IDBZD
InChIInChI=1S/C14H18N2O7/c17-6-8-9(18)10(19)11(20)13(23-8)16-14(22)15-12(21)7-4-2-1-3-5-7/h1-5,8-11,13,17-20H,6H2,(H2,15,16,21,22)/t8-,9-,10+,11-,13-/m1/s1
InChIKeyJSBCZGSPFATCOV-BZNQNGANSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH](NC(=O)NC(=O)c2ccccc2)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@@H](NC(=O)NC(=O)c2ccccc2)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04O=C(NC1OC(C(O)C(O)C1O)CO)NC(=O)c2ccccc2
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(=O)NC(=O)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(=O)NC(=O)NC2C(C(C(C(O2)CO)O)O)O
FormulaC14 H18 N2 O7
NameN-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine;
N-BENZOYL-N'-BETA-D-GLUCOPYRANOSYL UREA;
N-[(phenylcarbonyl)carbamoyl]-beta-D-glucosylamine;
N-[(phenylcarbonyl)carbamoyl]-D-glucosylamine;
N-[(phenylcarbonyl)carbamoyl]-glucosylamine
ChEMBLCHEMBL489799
DrugBankDB04295
ZINCZINC000006578607
PDB chain1k08 Chain A Residue 998 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1k08 Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies.
Resolution2.26 Å
Binding residue
(original residue number in PDB)		E88 G135 L136 N282 D283 H341 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		E76 G123 L124 N270 D271 H321 H357 N464 E652 S654 G655
Annotation score1
Binding affinityMOAD: Ki=4.6uM
PDBbind-CN: -logKd/Ki=5.34,Ki=4.6uM
BindingDB: Ki=4600nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H357 K548 R549 K554 T656 K660
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:1k08, PDBe:1k08, PDBj:1k08
PDBsum1k08
PubMed11895439
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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