Structure of PDB 5dc2 Chain A Binding Site BS01

Receptor Information
>5dc2 Chain A (length=352) Species: 83331 (Mycobacterium tuberculosis CDC1551) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRL
SPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPY
VMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNN
REVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIA
TADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDS
STYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCL
NVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGN
AK
Ligand information
Ligand ID58U
InChIInChI=1S/C8H10O5/c1-5(6(10)2-3-9)4-7(11)8(12)13/h3,5H,2,4H2,1H3,(H,12,13)/t5-/m0/s1
InChIKeyJDEHLHSRIXMJEO-YFKPBYRVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H](CC(=O)C(O)=O)C(=O)CC=O
OpenEye OEToolkits 2.0.5C[C@@H](CC(=O)C(=O)O)C(=O)CC=O
CACTVS 3.385C[CH](CC(=O)C(O)=O)C(=O)CC=O
OpenEye OEToolkits 2.0.5CC(CC(=O)C(=O)O)C(=O)CC=O
ACDLabs 12.01OC(C(CC(C(=O)CC=O)C)=O)=O
FormulaC8 H10 O5
Name(4S)-4-methyl-2,5,7-trioxoheptanoic acid
ChEMBL
DrugBank
ZINCZINC000584905131
PDB chain5dc2 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dc2 Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.
Resolution2.182 Å
Binding residue
(original residue number in PDB)		Y318 G332 H336 W340 S351 H352 G353 C354 N356
Binding residue
(residue number reindexed from 1)		Y263 G277 H281 W285 S296 H297 G298 C299 N301
Annotation score1
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:5dc2, PDBe:5dc2, PDBj:5dc2
PDBsum5dc2
PubMed28545389
UniProtI6Y9J2|LDT2_MYCTU L,D-transpeptidase 2 (Gene Name=ldtB)

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