Structure of PDB 3ukd Chain A Binding Site BS02

Receptor Information
>3ukd Chain A (length=191) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSKDGE
MIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNSWEE
NMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFNTFN
VQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSMGF
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 chain3ukd 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

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PDB3ukd Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
Resolution1.9 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)		G35 L38 R39 E60 I61 V62 G87 R90 R134 R145
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K19 R93 R131 R137 R148
Catalytic site (residue number reindexed from 1) K16 R90 R128 R134 R145
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ukd, PDBe:3ukd, PDBj:3ukd
PDBsum3ukd
PubMed9280438
UniProtP20425|KCY_DICDI UMP-CMP kinase (Gene Name=pyrK)

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