Structure of PDB 1ymx Chain B Binding Site BS01

Receptor Information
>1ymx Chain B (length=261) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAA
AAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAAL
QYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDP
RDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPT
SWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVL
ASAARIIAEGL
Ligand information
Ligand ID1QL
InChIInChI=1S/C16H19N3O7S2/c1-25-16(8-20,19-11(21)5-10-3-2-4-27-10)14-18-12(13(22)23)9(7-28-14)6-26-15(17)24/h2-4,8,14,18H,5-7H2,1H3,(H2,17,24)(H,19,21)(H,22,23)/t14-,16+/m1/s1
InChIKeyIYZWSAWEHPQLHS-ZBFHGGJFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CO[C](NC(=O)Cc1sccc1)(C=O)[CH]2NC(=C(COC(N)=O)CS2)C(O)=O
OpenEye OEToolkits 1.7.6COC(C=O)(C1NC(=C(CS1)COC(=O)N)C(=O)O)NC(=O)Cc2cccs2
CACTVS 3.370CO[C@@](NC(=O)Cc1sccc1)(C=O)[C@@H]2NC(=C(COC(N)=O)CS2)C(O)=O
ACDLabs 12.01O=CC(OC)(NC(=O)Cc1sccc1)C2SCC(=C(N2)C(=O)O)COC(=O)N
OpenEye OEToolkits 1.7.6CO[C@@](C=O)([C@@H]1NC(=C(CS1)COC(=O)N)C(=O)O)NC(=O)Cc2cccs2
FormulaC16 H19 N3 O7 S2
Name(2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid;
Cefoxitin, bound form
ChEMBL
DrugBank
ZINC
PDB chain1ymx Chain B Residue 1002 [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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PDB1ymx Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M beta-Lactamases.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S70 K73 N104 Y105 S130 N132 E166 N170 T235 G236 S237 G238 D240
Binding residue
(residue number reindexed from 1)		S43 K46 N77 Y78 S103 N105 E139 N143 T208 G209 S210 G211 D212
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 S237
Catalytic site (residue number reindexed from 1) S43 K46 S103 E139 K207 S210
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
Biological Process
GO:0017001 antibiotic catabolic process
GO:0030655 beta-lactam antibiotic catabolic process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1ymx, PDBe:1ymx, PDBj:1ymx
PDBsum1ymx
PubMed15826180
UniProtQ9L5C8

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