Structure of PDB 3dd1 Chain B Binding Site BS01

Receptor Information
>3dd1 Chain B (length=805) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQQ
HYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEEL
EEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIRD
GWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVVL
ALPYDTPVPGYMNNTVNTMRLWSARAPNDFNLRDFNVGDYIQAVLDRNLA
ENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFGSTGTV
FDAFPDQVAIQLNDTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYT
NHTVLPEALERWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRL
RRMSLIEEEGSKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELE
PDKFQNKTNGITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFL
GDDVFLRELAKVKQENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKR
QLLNCLHVITMYNRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITS
VADVVNNDPMVGSKLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASG
TGNMKFMLNGALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKG
YEAKEYYEALPELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFA
DYEAYVKCQDKVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIW
NVEPS
Ligand information
Ligand ID25D
InChIInChI=1S/C30H35N3O4/c1-18-14-19(2)26(20(3)15-18)32-29(37)31-25-17-22-11-9-8-10-21(22)16-24(25)27(34)33-30(4,28(35)36)23-12-6-5-7-13-23/h8-11,14-17,23H,5-7,12-13H2,1-4H3,(H,33,34)(H,35,36)(H2,31,32,37)/t30-/m0/s1
InChIKeyZYHGLTOSKWXGQM-PMERELPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc(C)c(NC(=O)Nc2cc3ccccc3cc2C(=O)N[C](C)(C4CCCCC4)C(O)=O)c(C)c1
OpenEye OEToolkits 1.5.0Cc1cc(c(c(c1)C)NC(=O)Nc2cc3ccccc3cc2C(=O)NC(C)(C4CCCCC4)C(=O)O)C
OpenEye OEToolkits 1.5.0Cc1cc(c(c(c1)C)NC(=O)Nc2cc3ccccc3cc2C(=O)N[C@@](C)(C4CCCCC4)C(=O)O)C
CACTVS 3.341Cc1cc(C)c(NC(=O)Nc2cc3ccccc3cc2C(=O)N[C@@](C)(C4CCCCC4)C(O)=O)c(C)c1
ACDLabs 10.04O=C(Nc1c(cc(cc1C)C)C)Nc3cc4c(cc3C(=O)NC(C(=O)O)(C)C2CCCCC2)cccc4
FormulaC30 H35 N3 O4
Name2-cyclohexyl-N-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-D-alanine
ChEMBLCHEMBL482146
DrugBank
ZINCZINC000040936160
PDB chain3dd1 Chain A Residue 905 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dd1 Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.
Resolution2.57 Å
Binding residue
(original residue number in PDB)		K41 D42 V45
Binding residue
(residue number reindexed from 1)		K19 D20 V23
Annotation score1
Binding affinityBindingDB: IC50=10nM
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:0002060 purine nucleobase binding
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005536 D-glucose binding
GO:0008184 glycogen phosphorylase activity
GO:0016208 AMP binding
GO:0016757 glycosyltransferase activity
GO:0019842 vitamin binding
GO:0030170 pyridoxal phosphate binding
GO:0030246 carbohydrate binding
GO:0032052 bile acid binding
GO:0042802 identical protein binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process
GO:0009617 response to bacterium
GO:0042593 glucose homeostasis
GO:0070266 necroptotic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dd1, PDBe:3dd1, PDBj:3dd1
PDBsum3dd1
PubMed19138846
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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