Structure of PDB 3ddw Chain B Binding Site BS05

Receptor Information
>3ddw Chain B (length=800) 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
ALPYDTPVPGYMNNTVNTMRLWSARAPNDFNLRDGDYIQAVLDRNLAENI
SRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFGGTVFDAFP
DQVAIQLNDTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVL
PEALERWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSL
IEEEGSKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQ
NKTNGITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVF
LRELAKVKQENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNC
LHVITMYNRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVV
NNDPMVGSKLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMK
FMLNGALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKE
YYEALPELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAY
VKCQDKVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPS
Ligand information
Ligand ID055
InChIInChI=1S/C27H22ClN3O4/c1-16-8-7-13-21(28)23(16)31-27(35)29-22-15-19-12-6-5-11-18(19)14-20(22)25(32)30-24(26(33)34)17-9-3-2-4-10-17/h2-15,24H,1H3,(H,30,32)(H,33,34)(H2,29,31,35)/t24-/m0/s1
InChIKeyKRIVDSIBMDCVLL-DEOSSOPVSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cccc(Cl)c1NC(=O)Nc2cc3ccccc3cc2C(=O)N[CH](C(O)=O)c4ccccc4
OpenEye OEToolkits 1.5.0Cc1cccc(c1NC(=O)Nc2cc3ccccc3cc2C(=O)NC(c4ccccc4)C(=O)O)Cl
OpenEye OEToolkits 1.5.0Cc1cccc(c1NC(=O)Nc2cc3ccccc3cc2C(=O)N[C@@H](c4ccccc4)C(=O)O)Cl
ACDLabs 10.04Clc4cccc(c4NC(=O)Nc3cc1ccccc1cc3C(=O)NC(c2ccccc2)C(=O)O)C
CACTVS 3.341Cc1cccc(Cl)c1NC(=O)Nc2cc3ccccc3cc2C(=O)N[C@H](C(O)=O)c4ccccc4
FormulaC27 H22 Cl N3 O4
Name(2S)-{[(3-{[(2-chloro-6-methylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]amino}(phenyl)ethanoic acid
ChEMBL
DrugBank
ZINCZINC000058660719
PDB chain3ddw Chain B Residue 906 [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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PDB3ddw 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.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		W67 Q71 Q72 R193 D227 R310
Binding residue
(residue number reindexed from 1)		W45 Q49 Q50 R171 D205 R285
Annotation score1
Binding affinityMOAD: ic50=1067nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H347 K538 R539 K544 T646 K650
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:3ddw, PDBe:3ddw, PDBj:3ddw
PDBsum3ddw
PubMed19138846
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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