Structure of PDB 8pxz Chain A Binding Site BS01

Receptor Information

>8pxz Chain A (length=351) Species: 1773 (Mycobacterium tuberculosis)

LLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLS
PDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYV
MPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNR
EVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIAT
ADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSS
TYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLN
VSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNA
K

Ligand information

• Ligand ID: I1V
• InChI: InChI=1S/C12H25N5O4/c13-8(11(15)20)3-1-2-7(6-18)17-10(19)5-4-9(14)12(16)21/h7-9,18H,1-6,13-14H2,(H2,15,20)(H2,16,21)(H,17,19)/t7-,8+,9+/m0/s1
• InChIKey: JJMJHAUQDTZOGG-DJLDLDEBSA-N
• SMILES:
  CACTVS 3.385: N[C@H](CCC[C@@H](CO)NC(=O)CC[C@@H](N)C(N)=O)C(N)=O
  OpenEye OEToolkits 2.0.7: C(CC(CO)NC(=O)CCC(C(=O)N)N)CC(C(=O)N)N
  CACTVS 3.385: N[CH](CCC[CH](CO)NC(=O)CC[CH](N)C(N)=O)C(N)=O
  OpenEye OEToolkits 2.0.7: C(C[C@@H](CO)NC(=O)CC[C@H](C(=O)N)N)C[C@H](C(=O)N)N
• Formula: C12 H25 N5 O4
• Name: (2~{R})-2-azanyl-~{N}'-[(2~{S},6~{R})-6,7-bis(azanyl)-1-oxidanyl-7-oxidanylidene-heptan-2-yl]pentanediamide
• PDB chain: 8pxz Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pxz Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with natural substrate
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): Y318 T320 S331 G332 V333 H336 H352 G353 C354
• Binding residue (residue number reindexed from 1): Y262 T264 S275 G276 V277 H280 H296 G297 C298
• Annotation score: 1

External links

• PDB: RCSB:8pxz, PDBe:8pxz, PDBj:8pxz
• PDBsum: 8pxz
• UniProt: O53223|LDT2_MYCTO L,D-transpeptidase 2 (Gene Name=ldtB)