Structure of PDB 4die Chain A Binding Site BS01

Receptor Information
>4die Chain A (length=204) Species: 561007 (Mycobacteroides abscessus ATCC 19977) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMVVAVDGPSGTGKSSVAKELARQLGASYLDTGAMYRIVTLWVLRAGVDL
TDPAAIAAATDQVPMSVSSDPDAQTALLAGEDVSVPIRGNEVTGAVSAVS
AVPAVRERLVRQQRELAESSGAVVVEGRDIGTVVLPDADVKIYLTASAQA
RAQRRNAQNVLADVQRRDHLDSTRLRPAEDALEVDTSDMTQEQVVAHLLD
LVRT
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 chain4die Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4die Increasing the structural coverage of tuberculosis drug targets.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		G31 Y34 V94 S95 S98 R104 R126
Binding residue
(residue number reindexed from 1)		G33 Y36 V96 S97 S100 R106 R128
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.25: (d)CMP kinase.
Gene Ontology
Molecular Function
GO:0004127 (d)CMP kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0036430 CMP kinase activity
GO:0036431 dCMP kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006220 pyrimidine nucleotide metabolic process
GO:0009058 biosynthetic process
GO:0015949 nucleobase-containing small molecule interconversion
GO:0016310 phosphorylation
GO:0044281 small molecule metabolic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4die, PDBe:4die, PDBj:4die
PDBsum4die
PubMed25613812
UniProtB1MB31

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