Structure of PDB 5j5d Chain A Binding Site BS01

Receptor Information
>5j5d Chain A (length=297) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSG
TTGESPTTTDGEKIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACA
AEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPI
EPDTIRALASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWL
AMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLCNAMSR
LGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR
Ligand information
Ligand ID6GT
InChIInChI=1S/C7H10O5/c8-5(7(11)12)3-1-2-4-6(9)10/h1-4H2,(H,9,10)(H,11,12)
InChIKeyHABHUTWTLGRDDU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(CCCCC(C(=O)O)=O)O
CACTVS 3.385OC(=O)CCCCC(=O)C(O)=O
OpenEye OEToolkits 2.0.4C(CCC(=O)O)CC(=O)C(=O)O
FormulaC7 H10 O5
Name2-oxoheptanedioic acid;
2-Ketopimelic acid
ChEMBLCHEMBL185075
DrugBank
ZINCZINC000002508023
PDB chain5j5d Chain A Residue 403 [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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PDB5j5d Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A18 T54 T55 Y143 R148 K171 G194
Binding residue
(residue number reindexed from 1)		A15 T51 T52 Y140 R145 K168 G191
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.68,IC50=21uM
Enzymatic activity
Catalytic site (original residue number in PDB) T54 Y117 Y143 R148 K171 I211
Catalytic site (residue number reindexed from 1) T51 Y114 Y140 R145 K168 I208
Enzyme Commision number 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.
Gene Ontology
Molecular Function
GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
GO:0044281 small molecule metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
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:5j5d, PDBe:5j5d, PDBj:5j5d
PDBsum5j5d
PubMed27501775
UniProtP9WP25|DAPA_MYCTU 4-hydroxy-tetrahydrodipicolinate synthase (Gene Name=dapA)

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