Structure of PDB 3q80 Chain B Binding Site BS02

Receptor Information
>3q80 Chain B (length=218) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVV
VAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLEPEFVLVHDAA
RALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAG
LRAVQTPQGFTTDLLLRSYQRLPAAEYTDDASLVEHIGGQVQVVDGDPLA
FKITTKLDLLLAQAIVRG
Ligand information
Ligand IDCDM
InChIInChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1
InChIKeyYFAUKWZNPVBCFF-XHIBXCGHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(CO)(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)O)O
CACTVS 3.341C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N
CACTVS 3.341C[C](O)(CO)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N
ACDLabs 10.04O=P(O)(OCC(O)C(O)(C)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O)O
FormulaC14 H25 N3 O14 P2
Name4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
ChEMBLCHEMBL1231708
DrugBankDB03687
ZINCZINC000008419042
PDB chain3q80 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3q80 Crystal Structure of Mycobacterium tuberculosis 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD): a candidate antitubercular drug target
Resolution2.0 Å
Binding residue
(original residue number in PDB)		P13 A14 A15 G16 K27 G80 S81 N82 R83 T86 D107 R110 V163 T165 T191 K215
Binding residue
(residue number reindexed from 1)		P8 A9 A10 G11 K22 G75 S76 N77 R78 T81 D98 R101 V154 T156 T178 K202
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.60: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0002135 CTP binding
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0030145 manganese ion binding
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
GO:0051484 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3q80, PDBe:3q80, PDBj:3q80
PDBsum3q80
PubMed
UniProtP9WKG9|ISPD_MYCTU 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (Gene Name=ispD)

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