Structure of PDB 4wpu Chain A Binding Site BS01

Receptor Information
>4wpu Chain A (length=599) Species: 419947 (Mycobacterium tuberculosis H37Ra) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMTSATIPGLDTAPTNHQGLLSWVEEVAELTQPDRVVFTDGSEEEFQRL
CDQLVEAGTFIRLNPEKHKNSYLALSDPSDVARVASRTYICSAKEIDAGP
TNNWMDPGEMRSIMKDLYRGCMRGRTMYVVPFCMGPLGAEDPKLGVEITD
SEYVVVSMRTMTRMGKAALEKMGDDGFFVKALHSVGAPLEPGQKDVAWPC
SETKYITHFPETREIWSYGSGYGGNALLGKKCYSLRIASAMAHDEGWLAE
HMLILKLISPENKAYYFAAAFPSACGKTNLAMLQPTIPGWRAETLGDDIA
WMRFGKDGRLYAVNPEFGFFGVAPGTNWKSNPNAMRTIAAGNTVFTNVAL
TDDGDVWWEGLEGDPQHLIDWKGNDWYFRETETNAAHPNSRYCTPMSQCP
ILAPEWDDPQGVPISGILFGGRRKTTVPLVTEARDWQHGVFIGATLGSEQ
NVRRDPMAMLPFLGYNVGDYFQHWINLGKHADESKLPKVFFVNWFRRGDD
GRFLWPGFGENSRVLKWIVDRIEHKAGGATTPIGTVPAVEDLDLDGLDVD
AADVAAALAVDADEWRQELPLIEEWLQFVGEKLPTGVKDEFDALKERLG
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 chain4wpu 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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PDB4wpu Crystal Structure of E83A mutant of Mtb PEPCK in complex with PEP and GDP
Resolution2.26 Å
Binding residue
(original residue number in PDB)		A272 G274 K275 T276 N277 R420 W501 F502 F510 F515
Binding residue
(residue number reindexed from 1)		A274 G276 K277 T278 N279 R422 W494 F495 F503 F508
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R81 Y220 K229 H249 S271 C273 D296 R389
Catalytic site (residue number reindexed from 1) R83 Y222 K231 H251 S273 C275 D298 R391
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:0019543 propionate catabolic process
GO:0033993 response to lipid
GO:0042594 response to starvation
GO:0046327 glycerol biosynthetic process from pyruvate
GO:0071333 cellular response to glucose stimulus
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4wpu, PDBe:4wpu, PDBj:4wpu
PDBsum4wpu
PubMed
UniProtA5TYT6|PCKG_MYCTA Phosphoenolpyruvate carboxykinase [GTP] (Gene Name=pckG)

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