Structure of PDB 6rrm Chain A Binding Site BS01

Receptor Information
>6rrm Chain A (length=351) Species: 83331 (Mycobacterium tuberculosis CDC1551) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLS
PDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYV
MPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNR
EVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIAT
ADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSS
TYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLN
VSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNA
K
Ligand information
Ligand ID9JT
InChIInChI=1S/C13H11NOSe/c15-13(11-8-4-5-9-12(11)16)14-10-6-2-1-3-7-10/h1-9,16H,(H,14,15)
InChIKeyPVPUYGNPKBMXGO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)NC(=O)c2ccccc2[SeH]
CACTVS 3.385[SeH]c1ccccc1C(=O)Nc2ccccc2
ACDLabs 12.01O=C(Nc1ccccc1)c1ccccc1[SeH]
FormulaC13 H11 N O Se
NameN-phenyl-2-selanylbenzamide;
~{N}-phenyl-2-selanyl-benzamide;
Ebselen, bound form
ChEMBL
DrugBank
ZINC
PDB chain6rrm Chain A Residue 504 [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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PDB6rrm Targeting the Mycobacterium tuberculosis transpeptidase LdtMt2with cysteine-reactive inhibitors including ebselen.
Resolution1.64 Å
Binding residue
(original residue number in PDB)		M303 N316 Y318 V322 H336 H352 C354
Binding residue
(residue number reindexed from 1)		M247 N260 Y262 V266 H280 H296 C298
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.84,IC50=0.143uM
Enzymatic activity
Enzyme Commision number 2.3.2.-
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0046872 metal ion binding
GO:0071972 peptidoglycan L,D-transpeptidase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0018104 peptidoglycan-protein cross-linking
GO:0071555 cell wall organization
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:6rrm, PDBe:6rrm, PDBj:6rrm
PDBsum6rrm
PubMed31380528
UniProtI6Y9J2|LDT2_MYCTU L,D-transpeptidase 2 (Gene Name=ldtB)

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