Structure of PDB 4zdq Chain A Binding Site BS01

Receptor Information
>4zdq Chain A (length=230) Species: 271848 (Burkholderia thailandensis E264) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TSRLFALIPCAGTGSRSGSALPKQYRTLAGRALLHYTLAAFDACSEFAQT
LVVISPDDAHFDARRFAGLRFAVRRCGGASRQASVMNGLIQLAEFGATDA
DWVLVHDAARPGITPALIRTLIGALKDDPVGGIVALPVADTLKRVPAGGD
AIERTESRNGLWQAQTPQMFRIGMLRDAIQRAQLEGRDLTDEASAIEWAG
HTPRVVQGSLRNFKVTYPEDFDLAEAILAH
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 chain4zdq Chain A Residue 301 [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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PDB4zdq Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
Resolution2.3 Å
Binding residue
(original residue number in PDB)		P10 C11 A12 G13 T14 G15 S16 R17 K24 A80 S81 R82 S85 D108 A109 K215
Binding residue
(residue number reindexed from 1)		P9 C10 A11 G12 T13 G14 S15 R16 K23 A79 S80 R81 S84 D107 A108 K214
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.60: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016779 nucleotidyltransferase activity
GO:0050518 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
GO:0070567 cytidylyltransferase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4zdq, PDBe:4zdq, PDBj:4zdq
PDBsum4zdq
PubMed38305785
UniProtQ2SWT6|ISPD_BURTA 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (Gene Name=ispD)

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