Structure of PDB 4rcg Chain A Binding Site BS01

Receptor Information
>4rcg Chain A (length=592) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLDTAPTNHQGLLSWVEEVAELTQPDRVVFTDGSEEEFQRLCDQLVEAGT
FIRLNPEKHKNSYLALSDPSDVARVESRTYICSAKEIDAGPTNNWMDPGE
MRSIMKDLYRGCMRGRTMYVVPFCMGPLGAEDPKLGVEITDSEYVVVSMR
TMTRMGKAALEKMGDDGFFVKALHSVGAPLEPGQKDVAWPCSETKYITHF
PETREIWSYGSGYGGNALLGKKCYSLRIASAMAHDEGWLAEHMLILKLIS
PENKAYYFAAAFPSACGKTNLAMLQPTIPGWRAETLGDDIAWMRFGKDGR
LYAVNPEFGFFGVAPGTNWKSNPNAMRTIAAGNTVFTNVALTDDGDVWWE
GLEGDPQHLIDWKGNDWYFRETETNAAHPNSRYCTPMSQCPILAPEWDDP
QGVPISGILFGGRRKTTVPLVTEARDWQHGVFIGATLGSEQTANVRRDPM
AMLPFLGYNVGDYFQHWINLGKHADEAKLPKVFFVNWFRRGDDGRFLWPG
FGENSRVLKWIVDRIEHKAGGATTPIGTVPAVEDLDLDGLDVDAADVAAA
LAVDADEWRQELPLIEEWLQFVGEKLPTGVKDEFDALKERLG
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4rcg Chain A Residue 701 [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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PDB4rcg Structural and Functional Studies of Phosphoenolpyruvate Carboxykinase from Mycobacterium tuberculosis.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S271 A272 G274 K275 T276 N277 W501 F502 G514 F515
Binding residue
(residue number reindexed from 1)		S264 A265 G267 K268 T269 N270 W487 F488 G500 F501
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=5.03,Kd=9.3uM
Enzymatic activity
Catalytic site (original residue number in PDB) R81 Y220 K229 H249 S271 C273 D296 R389
Catalytic site (residue number reindexed from 1) R74 Y213 K222 H242 S264 C266 D289 R382
Enzyme Commision number 4.1.1.32: phosphoenolpyruvate carboxykinase (GTP).
Gene Ontology
Molecular Function
GO:0004611 phosphoenolpyruvate carboxykinase activity
GO:0004613 phosphoenolpyruvate carboxykinase (GTP) activity
GO:0005525 GTP binding
GO:0016831 carboxy-lyase activity
GO:0017076 purine nucleotide binding
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006094 gluconeogenesis
GO:0006107 oxaloacetate metabolic process
GO:0010106 cellular response to iron ion starvation
GO:0019543 propionate catabolic process
GO:0033993 response to lipid
GO:0042594 response to starvation
GO:0046327 glycerol biosynthetic process from pyruvate
GO:0052572 response to host immune response
GO:0071333 cellular response to glucose stimulus
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4rcg, PDBe:4rcg, PDBj:4rcg
PDBsum4rcg
PubMed25798914
UniProtP9WIH3|PCKG_MYCTU Phosphoenolpyruvate carboxykinase [GTP] (Gene Name=pckG)

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