Structure of PDB 1qf9 Chain A Binding Site BS03

Receptor Information
>1qf9 Chain A (length=194) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSK
DGEMIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNS
WEENMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFN
TFNVQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSMGF
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain1qf9 Chain A Residue 196 [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]
PDB1qf9 pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G38 L41 R42 E63 I64 V65 G90 R93 R137 R148
Binding residue
(residue number reindexed from 1)		G38 L41 R42 E63 I64 V65 G90 R93 R137 R148
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K19 R93 R131 R137 R148
Catalytic site (residue number reindexed from 1) K19 R93 R131 R137 R148
Enzyme Commision number 2.7.4.14: UMP/CMP kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004127 (d)CMP kinase activity
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0019205 nucleobase-containing compound kinase activity
GO:0033862 UMP kinase activity
GO:0036430 CMP kinase activity
GO:0036431 dCMP 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:0043100 pyrimidine nucleobase salvage
GO:0043173 nucleotide salvage
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:1qf9, PDBe:1qf9, PDBj:1qf9
PDBsum1qf9
PubMed10426946
UniProtP20425|KCY_DICDI UMP-CMP kinase (Gene Name=pyrK)

[Back to BioLiP]