Structure of PDB 3zcv Chain A Binding Site BS02

Receptor Information
>3zcv Chain A (length=810) 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
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNF
DAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTN
HTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLR
RMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEP
HKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVD
DEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQ
LLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAI
GDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGT
GNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGY
NAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFAD
YEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWG
VEPSRQRLPA
Ligand information
Ligand IDN85
InChIInChI=1S/C16H19N3O7/c20-6-10-11(21)12(22)13(23)15(26-10)19-16(25)18-14(24)9-5-7-3-1-2-4-8(7)17-9/h1-5,10-13,15,17,20-23H,6H2,(H2,18,19,24,25)/t10-,11-,12+,13-,15-/m1/s1
InChIKeyKAFZFGVMCHNQST-ZHZXCYKASA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H]1O[C@@H](NC(=O)NC(=O)c2[nH]c3ccccc3c2)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.9.2c1ccc2c(c1)cc([nH]2)C(=O)NC(=O)NC3C(C(C(C(O3)CO)O)O)O
OpenEye OEToolkits 1.9.2c1ccc2c(c1)cc([nH]2)C(=O)NC(=O)N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
ACDLabs 12.01O=C(NC1OC(C(O)C(O)C1O)CO)NC(=O)c3cc2ccccc2n3
CACTVS 3.385OC[CH]1O[CH](NC(=O)NC(=O)c2[nH]c3ccccc3c2)[CH](O)[CH](O)[CH]1O
FormulaC16 H19 N3 O7
NameN-[(1H-indol-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
ChEMBLCHEMBL2030479
DrugBank
ZINCZINC000084668998
PDB chain3zcv 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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PDB3zcv 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.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		G135 L136 N282 D283 H341 H377 A383 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N265 D266 H315 H351 A357 N458 E646 S648 G649
Annotation score1
Binding affinityBindingDB: IC50=4000nM,Ki=4000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H351 K542 R543 K548 T650 K654
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:3zcv, PDBe:3zcv, PDBj:3zcv
PDBsum3zcv
PubMed
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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