Structure of PDB 2tdt Chain A Binding Site BS01

Receptor Information
>2tdt Chain A (length=274) Species: 1765 (Mycobacterium tuberculosis variant bovis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKID
GQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQK
EGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCA
QIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGS
VISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCA
VIVKKVDAKTRGKVGINELLRTID
Ligand information
Ligand IDCOA
InChIInChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
InChIKeyRGJOEKWQDUBAIZ-IBOSZNHHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
ACDLabs 10.04O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC21 H36 N7 O16 P3 S
NameCOENZYME A
ChEMBLCHEMBL1213327
DrugBankDB01992
ZINCZINC000008551087
PDB chain2tdt Chain A Residue 280 [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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PDB2tdt The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S159 F183 G185 S203 M204 R217 K254 K259 T260 K263
Binding residue
(residue number reindexed from 1)		S159 F183 G185 S203 M204 R217 K254 K259 T260 K263
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D141 G166 E189
Catalytic site (residue number reindexed from 1) D141 G166 E189
Enzyme Commision number 2.3.1.117: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase.
Gene Ontology
Molecular Function
GO:0008666 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2tdt, PDBe:2tdt, PDBj:2tdt
PDBsum2tdt
PubMed9671504
UniProtP56220|DAPD_UNKP 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (Gene Name=dapD)

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