Structure of PDB 4gnp Chain A Binding Site BS01

Receptor Information
>4gnp Chain A (length=605) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAH
MQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSG
QSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIE
LTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNN
WACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEG
WLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVG
DDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTN
VAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTP
ASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAA
MRSEGGGIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWF
RKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLK
GLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQ
RISQM
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 chain4gnp 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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PDB4gnp The {Omega}-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function.
Resolution1.744 Å
Binding residue
(original residue number in PDB)		A287 G289 K290 T291 N292 R436 W516 F517 F530
Binding residue
(residue number reindexed from 1)		A278 G280 K281 T282 N283 R427 W499 F500 F513
Annotation score4
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 Y226 K235 H255 S277 C279 D302 R396
Enzyme Commision number 2.7.11.-
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:0017076 purine nucleotide binding
Biological Process
GO:0006094 gluconeogenesis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4gnp, PDBe:4gnp, PDBj:4gnp
PDBsum4gnp
PubMed23127136
UniProtP07379|PCKGC_RAT Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (Gene Name=Pck1)

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