Structure of PDB 16pk Chain A Binding Site BS01

Receptor Information
>16pk Chain A (length=415) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEG
GSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKRLSELLL
RPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKI
LASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVL
GNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYS
IGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITE
DQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTF
AIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLEL
LEGKTLPGVTVLDDK
Ligand information
Ligand IDBIS
InChIInChI=1S/C15H22F4N5O12P3/c16-14(17,37(27,28)29)2-1-3-15(18,19)38(30,31)36-39(32,33)34-4-7-9(25)10(26)13(35-7)24-6-23-8-11(20)21-5-22-12(8)24/h5-7,9-10,13,25-26H,1-4H2,(H,30,31)(H,32,33)(H2,20,21,22)(H2,27,28,29)/t7-,9-,10-,13-/m1/s1
InChIKeyVWQBAZQMKBHYJA-QYVSTXNMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(C(CCCC(F)(F)P(=O)(O)O)(F)F)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)CCCC(F)(F)[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)C(F)(F)CCCC(F)(F)[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(C(CCCC(F)(F)P(=O)(O)O)(F)F)O)O)O)N
ACDLabs 10.04FC(F)(P(=O)(O)O)CCCC(F)(F)P(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 F4 N5 O12 P3
Name1,1,5,5-TETRAFLUOROPHOSPHOPENTYLPHOSPHONIC ACID ADENYLATE ESTER
ChEMBLCHEMBL1160562
DrugBank
ZINCZINC000024411934
PDB chain16pk Chain A Residue 499 [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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PDB16pk A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G217 A218 K223 A242 Y245 L315 P340 G342 V343 E345 G397 G398 G399
Binding residue
(residue number reindexed from 1)		G213 A214 K219 A238 Y241 L311 P336 G338 V339 E341 G393 G394 G395
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=5.22,Ki=6uM
Enzymatic activity
Catalytic site (original residue number in PDB) R39 K219 G376 G399
Catalytic site (residue number reindexed from 1) R35 K215 G372 G395
Enzyme Commision number 2.7.2.3: phosphoglycerate kinase.
Gene Ontology
Molecular Function
GO:0004618 phosphoglycerate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0043531 ADP binding
Biological Process
GO:0006094 gluconeogenesis
GO:0006096 glycolytic process
GO:0016310 phosphorylation
Cellular Component
GO:0005829 cytosol
GO:0020015 glycosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:16pk, PDBe:16pk, PDBj:16pk
PDBsum16pk
PubMed9642090
UniProtP07378|PGKC_TRYBB Phosphoglycerate kinase, glycosomal

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