Structure of PDB 6iyw Chain A Binding Site BS01

Receptor Information
>6iyw Chain A (length=266) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKI
TTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGE
DNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANG
IYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPW
SVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDG
LGDWNIPWDQWRAGNA
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 A 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 H352 C354
Binding residue
(residue number reindexed from 1)
M163 Y168 Y178 S191 H212 C214
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.23,Kd=58.8nM
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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