Structure of PDB 8g6p Chain A Binding Site BS02

Receptor Information
>8g6p Chain A (length=508) Species: 1797 (Mycolicibacterium thermoresistibile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMMNLRPSDPVGASLRHLAEQVHAVPIGSVEVPDLHISGITLRSQDARRG
DLFAALAGASAHGADHAADAVARGAVAVLTDSAGATRLDGTVPAPVLVHP
NPRTVLGELAATVYGRPADRLRVIGITGTSGKTTTAYLVEAGLRAADRVP
GLIGTVGVRIDGMDEPSALTTPEAPDLQALLAVMADRGVDTVVMEVSSHA
LSLHRVDGVRFAVGGFTNLSRDHLDFHPTMADYFAAKARLFDPQAPTCAE
RSVICIDDEAGRAMLAGAHRPVSVSATGQRADWVAEDVRFAGPTAQDFTA
VDPAGVRHRLRVGLPGRFNIANCLLAVALLDAVGVSPAQAAPGLRTATVP
GRLEPVDRGQDFLALVDYAHKPGALSAVLDSLRASATGRLAVVFGAGGNR
DPGKREEMGRVAAERADLVVVTDDNPRDEDPAAIRAAIVAGAKSVAGQAQ
IVEIADRREAIDHAVRWAGAGDVVLIAGKGHESGQTRGGQTRPFDDRAEL
AAALVART
Ligand information
Ligand IDAPI
InChIInChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
InChIKeyGMKMEZVLHJARHF-SYDPRGILSA-N
SMILES
SoftwareSMILES
CACTVS 3.370N[CH](CCC[CH](N)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.2C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
OpenEye OEToolkits 1.7.2C(CC(C(=O)O)N)CC(C(=O)O)N
CACTVS 3.370N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCC(C(=O)O)N
FormulaC7 H14 N2 O4
Name2,6-DIAMINOPIMELIC ACID
ChEMBLCHEMBL415306
DrugBank
ZINCZINC000001532722
PDB chain8g6p Chain A Residue 809 [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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PDB8g6p The crystal structure of Mycobacterium thermoresistibile MurE ligase reveals the binding mode of the substrate m-diaminopimelate.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		H368 R398 D422 N423 R425 G476 E480
Binding residue
(residue number reindexed from 1)		H370 R400 D424 N425 R427 G478 E482
Annotation score5
Enzymatic activity
Enzyme Commision number 6.3.2.13: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005524 ATP binding
GO:0008765 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
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:8g6p, PDBe:8g6p, PDBj:8g6p
PDBsum8g6p
PubMed36944394
UniProtG7CMG5

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