Structure of PDB 1m51 Chain A Binding Site BS02

Receptor Information
>1m51 Chain A (length=603) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLSAKVVQGSLDSLPQAVREFLENNAELCQPDHIHICDGSEEENGRLLGQ
MEEEGILRRLKKYDNCWLALTDPRDVARIESKTVIVTQEQRDTVPIPKTG
LSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSSKIGIELT
DSPYVVASMRIMTRMGTPVLEALGDGEFVKCLHSVGCPLPLQKPLVNNWP
CNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRMASRLAKEEGWL
AEHMLVLGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDD
IAWMKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVA
ETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPAS
QCPIIDAAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMR
SEAKIIMHDPFAMRPFFGYNFGKYLAHWLSMAQHPAAKLPKIFHVNWFRK
DKEGKFLWPGFGENSRVLEWMFNRIDGKASTKLTPIGYIPKEDALNLKGL
GHINMMELFSISKEFWDKEVEDIEKYLVDQVNADLPCEIEREILALKQRI
SQM
Ligand information
Ligand IDTSX
InChIInChI=1S/C21H25N5O3/c1-4-6-12-25-19-18(20(28)26(11-5-2)21(25)29)23-17(24-19)13-15-7-9-16(10-8-15)22-14(3)27/h5,7-10H,2,4,6,11-13H2,1,3H3,(H,22,27)(H,23,24)
InChIKeyXFOWZKUTPKXWIE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCN1c2c([nH]c(n2)Cc3ccc(cc3)NC(=O)C)C(=O)N(C1=O)CC=C
CACTVS 3.341CCCCN1C(=O)N(CC=C)C(=O)c2[nH]c(Cc3ccc(NC(C)=O)cc3)nc12
ACDLabs 10.04O=C(Nc1ccc(cc1)Cc3nc2N(C(=O)N(C(=O)c2n3)C\C=C)CCCC)C
FormulaC21 H25 N5 O3
NameN-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE;
1-ALLYL-3-BUTYL-8-(N-ACETYL-4-AMINOBENZYL)-XANTHINE
ChEMBLCHEMBL120293
DrugBankDB03267
ZINCZINC000015677757
PDB chain1m51 Chain A Residue 1001 [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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PDB1m51 X-ray Structures of two xanthine inhibitors bound to PEPCK and N-3 modifications of substituted 1,8-Dibenzylxanthines
Resolution2.25 Å
Binding residue
(original residue number in PDB)		N292 L293 W516 F517 F525 P528 F530 N533
Binding residue
(residue number reindexed from 1)		N281 L282 W497 F498 F506 P509 F511 N514
Annotation score1
Binding affinityMOAD: ic50=18.8uM
PDBbind-CN: -logKd/Ki=4.73,IC50=18.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) R87 Y235 K244 H264 S286 C288 D311 R405
Catalytic site (residue number reindexed from 1) R78 Y224 K233 H253 S275 C277 D300 R394
Enzyme Commision number 2.7.11.-
4.1.1.32: phosphoenolpyruvate carboxykinase (GTP).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004611 phosphoenolpyruvate carboxykinase activity
GO:0004613 phosphoenolpyruvate carboxykinase (GTP) activity
GO:0005525 GTP binding
GO:0016301 kinase activity
GO:0016831 carboxy-lyase activity
GO:0017076 purine nucleotide binding
GO:0019003 GDP binding
GO:0030145 manganese ion binding
GO:0031406 carboxylic acid binding
GO:0046872 metal ion binding
GO:0106264 protein serine kinase activity (using GTP as donor)
Biological Process
GO:0006006 glucose metabolic process
GO:0006094 gluconeogenesis
GO:0006107 oxaloacetate metabolic process
GO:0006629 lipid metabolic process
GO:0009617 response to bacterium
GO:0014823 response to activity
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0019543 propionate catabolic process
GO:0031667 response to nutrient levels
GO:0032496 response to lipopolysaccharide
GO:0032868 response to insulin
GO:0032869 cellular response to insulin stimulus
GO:0033993 response to lipid
GO:0042593 glucose homeostasis
GO:0042594 response to starvation
GO:0043382 positive regulation of memory T cell differentiation
GO:0043648 dicarboxylic acid metabolic process
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046166 glyceraldehyde-3-phosphate biosynthetic process
GO:0046327 glycerol biosynthetic process from pyruvate
GO:0046889 positive regulation of lipid biosynthetic process
GO:0046890 regulation of lipid biosynthetic process
GO:0051365 cellular response to potassium ion starvation
GO:0070365 hepatocyte differentiation
GO:0070741 response to interleukin-6
GO:0071300 cellular response to retinoic acid
GO:0071320 cellular response to cAMP
GO:0071332 cellular response to fructose stimulus
GO:0071333 cellular response to glucose stimulus
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor
GO:0071377 cellular response to glucagon stimulus
GO:0071456 cellular response to hypoxia
GO:0071474 cellular hyperosmotic response
GO:0071475 cellular hyperosmotic salinity response
GO:0071476 cellular hypotonic response
GO:0071477 cellular hypotonic salinity response
GO:0071549 cellular response to dexamethasone stimulus
GO:0072350 tricarboxylic acid metabolic process
GO:0097403 cellular response to raffinose
GO:1904628 cellular response to phorbol 13-acetate 12-myristate
GO:1904640 response to methionine
Cellular Component
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1m51, PDBe:1m51, PDBj:1m51
PDBsum1m51
PubMed14552798
UniProtP35558|PCKGC_HUMAN Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (Gene Name=PCK1)

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