Structure of PDB 3q07 Chain A Binding Site BS01

Receptor Information

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

TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCGTSKVMA
AAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAA
LQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGD
PRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLP
TSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDV
LASAARIIAEGL

Ligand information

• Ligand ID: WPP
• InChI: InChI=1S/C23H27N5O7S/c1-4-26-10-11-27(19(32)18(26)31)22(35)25-13(12-8-6-5-7-9-12)16(29)24-14-17(30)28-15(21(33)34)23(2,3)36-20(14)28/h5-9,13-15,20H,4,10-11H2,1-3H3,(H,24,29)(H,25,35)(H,33,34)/t13-,14-,15+,20-/m1/s1
• InChIKey: IVBHGBMCVLDMKU-GXNBUGAJSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@H]3[C@@H]4N(C3=O)[C@H](C(S4)(C)C)C(=O)O
  ACDLabs 12.01: O=C1C(=O)N(CC)CCN1C(=O)NC(c2ccccc2)C(=O)NC4C(=O)N3C(C(=O)O)C(SC34)(C)C
  OpenEye OEToolkits 1.7.0: CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC3C4N(C3=O)C(C(S4)(C)C)C(=O)O
  CACTVS 3.370: CCN1CCN(C(=O)N[CH](C(=O)N[CH]2[CH]3SC(C)(C)[CH](N3C2=O)C(O)=O)c4ccccc4)C(=O)C1=O
  CACTVS 3.370: CCN1CCN(C(=O)N[C@@H](C(=O)N[C@H]2[C@H]3SC(C)(C)[C@@H](N3C2=O)C(O)=O)c4ccccc4)C(=O)C1=O
• Formula: C23 H27 N5 O7 S
• Name: Piperacillin;
  (2S,5R,6R)-6-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}-3,3-dimethyl-7-oxo-4-thi a-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
• ChEMBL: CHEMBL702
• DrugBank: DB00319
• ZINC: ZINC000003913937
• PDB chain: 3q07 Chain A Residue 300

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 N104 S130 N132 P167 N170 T235 G236 S237 G238 D239
• Binding residue (residue number reindexed from 1): G44 N78 S104 N106 P141 N144 T209 G210 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