Structure of PDB 4ddy Chain B Binding Site BS01

Receptor Information

>4ddy Chain B (length=261) Species: 562 (Escherichia coli)

SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAA
AAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAAL
QYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDP
RDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPT
SWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVL
ASAARIIAEGL

Ligand information

• Ligand ID: DN6
• InChI: InChI=1S/C15H10F3N5O/c16-15(17,18)11-5-1-4-10(7-11)14(24)19-12-6-2-3-9(8-12)13-20-22-23-21-13/h1-8H,(H,19,24)(H,20,21,22,23)
• InChIKey: DVYVZPGHRBVPAG-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: FC(F)(F)c1cccc(c1)C(=O)Nc2cccc(c2)c3nnnn3
  CACTVS 3.370: FC(F)(F)c1cccc(c1)C(=O)Nc2cccc(c2)c3[nH]nnn3
  OpenEye OEToolkits 1.7.6: c1cc(cc(c1)NC(=O)c2cccc(c2)C(F)(F)F)c3[nH]nnn3
• Formula: C15 H10 F3 N5 O
• Name: N-[3-(1H-tetrazol-5-yl)phenyl]-3-(trifluoromethyl)benzamide
• ChEMBL: CHEMBL2031551
• ZINC: ZINC000006699658
• PDB chain: 4ddy Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ddy Structure-Based Design of Potent and Ligand-Efficient Inhibitors of CTX-M Class A Beta-Lactamase
• Resolution: 1.36 Å
• Binding residue (original residue number in PDB): K111 H112 A124 A125 Y129
• Binding residue (residue number reindexed from 1): K84 H85 A97 A98 Y102
• Annotation score: 1
• Binding affinity: MOAD: Ki=2.4uM

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

External links

• PDB: RCSB:4ddy, PDBe:4ddy, PDBj:4ddy
• PDBsum: 4ddy
• PubMed: 22296601
• UniProt: Q9L5C8