Structure of PDB 6iyw Chain D Binding Site BS01

Receptor Information
>6iyw Chain D (length=264) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKIT
TNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGED
NVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGI
YIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWS
VGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGL
GDWNIPWDQWRAGN
Ligand information
Ligand IDIM2
InChIInChI=1S/C12H19N3O4S/c1-7(17)8(5-16)9-4-10(11(15-9)12(18)19)20-3-2-14-6-13/h5-9,15,17H,2-4H2,1H3,(H2,13,14)(H,18,19)/t7-,8-,9-/m1/s1
InChIKeyUACUABDJLSUFFC-IWSPIJDZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6[H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O)C(=O)O
ACDLabs 12.01O=C(O)C1=C(SCCNC=[N@H])CC(N1)C(C=O)C(O)C
CACTVS 3.370C[C@@H](O)[C@@H](C=O)[C@H]1CC(=C(N1)C(O)=O)SCCNC=N
OpenEye OEToolkits 1.7.6CC(C(C=O)C1CC(=C(N1)C(=O)O)SCCNC=N)O
CACTVS 3.370C[CH](O)[CH](C=O)[CH]1CC(=C(N1)C(O)=O)SCCNC=N
FormulaC12 H19 N3 O4 S
Name(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid;
IMIPENEM, open form;
N-FORMIMIDOYL-THIENAMYCINE, open form
ChEMBL
DrugBank
ZINCZINC000103040234
PDB chain6iyw Chain D Residue 501 [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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PDB6iyw The 1-beta-methyl group confers a lower affinity of l,d-transpeptidase LdtMt2 for ertapenem than for imipenem.
Resolution1.6 Å
Binding residue
(original residue number in PDB)
M303 Y308 Y318 S331 G332 H352 C354
Binding residue
(residue number reindexed from 1)
M162 Y167 Y177 S190 G191 H211 C213
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.2.-
Gene Ontology
Molecular Function
GO:0016740 transferase activity

View graph for
Molecular Function
External links
PDB RCSB:6iyw, PDBe:6iyw, PDBj:6iyw
PDBsum6iyw
PubMed30686533
UniProtI6Y9J2|LDT2_MYCTU L,D-transpeptidase 2 (Gene Name=ldtB)

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