Structure of PDB 1kgq Chain A Binding Site BS02

Receptor Information
>1kgq 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 IDSCO
InChIInChI=1S/C25H41N8O19P3/c1-25(2,20(39)23(40)29-6-5-15(35)28-8-7-27-14(34)3-4-16(36)37)10-49-55(46,47)52-54(44,45)48-9-13-19(51-53(41,42)43)18(38)24(50-13)33-12-32-17-21(26)30-11-31-22(17)33/h11-13,18-20,24,38-39H,3-10H2,1-2H3,(H,27,34)(H,28,35)(H,29,40)(H,36,37)(H,44,45)(H,46,47)(H2,26,30,31)(H2,41,42,43)/t13-,18-,19-,20+,24-/m1/s1
InChIKeyWZEXTLJNSXEEHK-ITIYDSSPSA-N
SMILES
SoftwareSMILES
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)NCCNC(=O)CCC(=O)O)O
ACDLabs 10.04O=C(O)CCC(=O)NCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
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)NCCNC(=O)CCC(=O)O)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)NCCNC(=O)CCC(O)=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)NCCNC(=O)CCC(O)=O
FormulaC25 H41 N8 O19 P3
NameSUCCINAMIDE-COA
ChEMBL
DrugBankDB03905
ZINCZINC000195757410
PDB chain1kgq Chain A Residue 302 [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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PDB1kgq Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F183 G185 S203 M204 R217 V234 K254 K259 T260 K263
Binding residue
(residue number reindexed from 1)		F183 G185 S203 M204 R217 V234 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:1kgq, PDBe:1kgq, PDBj:1kgq
PDBsum1kgq
PubMed11910040
UniProtP56220|DAPD_UNKP 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (Gene Name=dapD)

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