Structure of PDB 1pkk Chain B Binding Site BS01

Receptor Information
>1pkk Chain B (length=177) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDL
SKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTT
NEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFD
KPVILYKNQRIGQLIFSKLLSPADVGY
Ligand information
Ligand IDDCP
InChIInChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL560403
DrugBankDB03258
ZINCZINC000008215945
PDB chain1pkk Chain B Residue 293 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1pkk Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii
Resolution1.77 Å
Binding residue
(original residue number in PDB)		H128 F138 T143
Binding residue
(residue number reindexed from 1)		H128 F138 T143
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S118 R122 A131 W133 E145
Catalytic site (residue number reindexed from 1) S118 R122 A131 W133 E145
Enzyme Commision number 3.5.4.30: dCTP deaminase (dUMP-forming).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008829 dCTP deaminase activity
GO:0016787 hydrolase activity
GO:0033973 dCTP deaminase (dUMP-forming) activity
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0006229 dUTP biosynthetic process
GO:0009117 nucleotide metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1pkk, PDBe:1pkk, PDBj:1pkk
PDBsum1pkk
PubMed12909016
UniProtQ57872|DCDB_METJA dCTP deaminase, dUMP-forming (Gene Name=dcd)

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