Structure of PDB 3q07 Chain A Binding Site BS02

Receptor Information

>3q07 Chain A (length=262) Species: 562 (Escherichia coli)

TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCGTSKVMA
AAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAA
LQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGD
PRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLP
TSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDV
LASAARIIAEGL

Ligand information

• Ligand ID: YPP
• InChI: InChI=1S/C23H29N5O8S/c1-4-27-10-11-28(19(31)18(27)30)22(36)25-13(12-8-6-5-7-9-12)16(29)24-14(20(32)33)17-26-15(21(34)35)23(2,3)37-17/h5-9,13-15,17,26H,4,10-11H2,1-3H3,(H,24,29)(H,25,36)(H,32,33)(H,34,35)/t13-,14+,15+,17-/m1/s1
• InChIKey: OKSUEATVFIVTFV-WBTNSWJXSA-N
• SMILES:
  CACTVS 3.370: CCN1CCN(C(=O)N[CH](C(=O)N[CH]([CH]2N[CH](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O
  OpenEye OEToolkits 1.7.0: CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@@H]([C@@H]3N[C@H](C(S3)(C)C)C(=O)O)C(=O)O
  ACDLabs 12.01: O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)NC(=O)N3C(=O)C(=O)N(CC)CC3
  OpenEye OEToolkits 1.7.0: CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C3NC(C(S3)(C)C)C(=O)O)C(=O)O
  CACTVS 3.370: CCN1CCN(C(=O)N[C@@H](C(=O)N[C@@H]([C@@H]2N[C@@H](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O
• Formula: C23 H29 N5 O8 S
• Name: Hydrolyzed piperacillin;
  (2R,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
• ZINC: ZINC000077312497
• PDB chain: 3q07 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3q07 CTX-M-9 S70G mutant in complex with piperacillin
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): G70 K73 N104 Y105 P167 N170 S237 G238 D239
• Binding residue (residue number reindexed from 1): G44 K47 N78 Y79 P141 N144 S211 G212 D213
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G70 K73 S130 E166 K234 S237
• Catalytic site (residue number reindexed from 1): G44 K47 S104 E140 K208 S211
• 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:3q07, PDBe:3q07, PDBj:3q07
• PDBsum: 3q07
• UniProt: Q9L5C8