Structure of PDB 2y6p Chain A Binding Site BS01

Receptor Information
>2y6p Chain A (length=231) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSE
RVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYE
EDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSP
IPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLE
NGIKIKVLITENYYHGVDTEEDLKIVEEKLK
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain2y6p Chain A Residue 1233 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y6p Evidence for a Two-Metal-Ion Mechanism in the Cytidyltransferase Kdsb, an Enzyme Involved in Lipopolysaccharide Biosynthesis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		A9 R10 S13 T14 R15 K19 P71 S72 G73 R76 G94
Binding residue
(residue number reindexed from 1)		A8 R9 S12 T13 R14 K18 P70 S71 G72 R75 G93
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.38: 3-deoxy-manno-octulosonate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0008690 3-deoxy-manno-octulosonate cytidylyltransferase activity
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0033468 CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2y6p, PDBe:2y6p, PDBj:2y6p
PDBsum2y6p
PubMed21826242
UniProtO66914|KDSB_AQUAE 3-deoxy-manno-octulosonate cytidylyltransferase (Gene Name=kdsB)

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