Structure of PDB 1ukz Chain A Binding Site BS01

Receptor Information
>1ukz Chain A (length=196) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAFSPDQVSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAGDLLRAEQGRA
GSQYGELIKNCIKEGQIVPQEITLALLRNAISDNVKANKHKFLIDGFPRK
MDQAISFERDIVESKFILFFDCPEDIMLERLLERGKTSGRSDDNIESIKK
RFNTFKETSMPVIEYFETKSKVVRVRCDRSVEDVYKDVQDAIRDSL
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-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)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[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)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1ukz Chain A Residue 205 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1ukz Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G26 G28 K29 G30 T31 R138 R142 R187 V189
Binding residue
(residue number reindexed from 1)		G18 G20 K21 G22 T23 R130 R134 R179 V181
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K29 R107 R142 R148 R159
Catalytic site (residue number reindexed from 1) K21 R99 R134 R140 R151
Enzyme Commision number 2.7.4.14: UMP/CMP kinase.
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0004127 (d)CMP kinase activity
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0019205 nucleobase-containing compound kinase activity
GO:0033862 UMP kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0016310 phosphorylation
GO:0046705 CDP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
GO:0072528 pyrimidine-containing compound biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ukz, PDBe:1ukz, PDBj:1ukz
PDBsum1ukz
PubMed7877173
UniProtP15700|KCY_YEAST Uridylate kinase (Gene Name=URA6)

[Back to BioLiP]