Structure of PDB 6iyv Chain B Binding Site BS01

Receptor Information
>6iyv Chain B (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 ID2RG
InChIInChI=1S/C22H27N3O7S/c1-10-17(15(9-26)11(2)27)25-18(22(31)32)19(10)33-14-7-16(23-8-14)20(28)24-13-5-3-4-12(6-13)21(29)30/h3-6,9-11,14-17,19,23,27H,7-8H2,1-2H3,(H,24,28)(H,29,30)(H,31,32)/t10-,11-,14+,15-,16+,17-,19+/m1/s1
InChIKeyRALHTEQYPKBGFO-SAGZMZRGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1C(C(=NC1C(C=O)C(C)O)C(=O)O)SC2CC(NC2)C(=O)Nc3cccc(c3)C(=O)O
OpenEye OEToolkits 1.7.6C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=O)O)S[C@H]2C[C@H](NC2)C(=O)Nc3cccc(c3)C(=O)O
CACTVS 3.370C[CH](O)[CH](C=O)[CH]1N=C([CH](S[CH]2CN[CH](C2)C(=O)Nc3cccc(c3)C(O)=O)[CH]1C)C(O)=O
ACDLabs 12.01O=C(O)c1cc(ccc1)NC(=O)C3NCC(SC2C(=NC(C2C)C(C=O)C(O)C)C(=O)O)C3
CACTVS 3.370C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@@H](S[C@@H]2CN[C@@H](C2)C(=O)Nc3cccc(c3)C(O)=O)[C@@H]1C)C(O)=O
FormulaC22 H27 N3 O7 S
Name(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid;
ERTAPENEM, bound form POST-ISOMERIZED
ChEMBL
DrugBank
ZINCZINC000058631760
PDB chain6iyv Chain B 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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PDB6iyv The 1-beta-methyl group confers a lower affinity of l,d-transpeptidase LdtMt2for ertapenem than for imipenem.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		M303 Y308 V310 Y318 G332 H352 G353 C354
Binding residue
(residue number reindexed from 1)		M162 Y167 V169 Y177 G191 H211 G212 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:6iyv, PDBe:6iyv, PDBj:6iyv
PDBsum6iyv
PubMed30686533
UniProtI6Y9J2|LDT2_MYCTU L,D-transpeptidase 2 (Gene Name=ldtB)

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