Structure of PDB 2rka Chain A Binding Site BS01

Receptor Information
>2rka Chain A (length=611) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEY
GRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTV
PIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPL
AKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLK
KPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASR
LAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGW
KVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQK
NTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPN
SRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHG
VFVGAAMRSEAKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKI
FHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKE
DALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERE
LRALKQRISQM
Ligand information
Ligand IDPGA
InChIInChI=1S/C2H5O6P/c3-2(4)1-8-9(5,6)7/h1H2,(H,3,4)(H2,5,6,7)
InChIKeyASCFNMCAHFUBCO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(=O)O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCC(=O)O
FormulaC2 H5 O6 P
Name2-PHOSPHOGLYCOLIC ACID
ChEMBLCHEMBL47181
DrugBankDB02726
ZINCZINC000003869735
PDB chain2rka Chain A Residue 623 [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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PDB2rka Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		R87 G237 K244 F333 R405
Binding residue
(residue number reindexed from 1)		R84 G234 K241 F330 R402
Annotation score1
Binding affinityMOAD: Ki=1mM
PDBbind-CN: -logKd/Ki=3.00,Ki=1mM
Enzymatic activity
Catalytic site (original residue number in PDB) R87 Y235 K244 H264 S286 C288 D311 R405
Catalytic site (residue number reindexed from 1) R84 Y232 K241 H261 S283 C285 D308 R402
Enzyme Commision number 2.7.11.-
4.1.1.32: phosphoenolpyruvate carboxykinase (GTP).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004550 nucleoside diphosphate kinase activity
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2rka, PDBe:2rka, PDBj:2rka
PDBsum2rka
PubMed18197707
UniProtP07379|PCKGC_RAT Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (Gene Name=Pck1)

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