Structure of PDB 2hdq Chain A Binding Site BS01

Receptor Information

>2hdq Chain A (length=358) Species: 83333 (Escherichia coli K-12)

APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQP
VTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNG
ITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANS
SIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGY
REGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQ
LAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITP
PTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAA
WQILNALQ

Ligand information

• Ligand ID: C21
• InChI: InChI=1S/C5H4O2S/c6-5(7)4-2-1-3-8-4/h1-3H,(H,6,7)
• InChIKey: QERYCTSHXKAMIS-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(sc1)C(=O)O
  CACTVS 3.341: OC(=O)c1sccc1
  ACDLabs 10.04: O=C(O)c1sccc1
• Formula: C5 H4 O2 S
• Name: THIOPHENE-2-CARBOXYLIC ACID
• ChEMBL: CHEMBL1222314
• ZINC: ZINC000000157468
• PDB chain: 2hdq Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2hdq Deconstructing fragment-based inhibitor discovery
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): R148 Y150 K290
• Binding residue (residue number reindexed from 1): R145 Y147 K287
• Annotation score: 1
• Binding affinity: MOAD: Ki=40mM
  PDBbind-CN: -logKd/Ki=1.40,Ki=40mM
  BindingDB: Ki=40000000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): S64 K67 Y112 A114 V121 Y150 G156 E272 K315 A318
• Catalytic site (residue number reindexed from 1): S61 K64 Y109 A111 V118 Y147 G153 E269 K312 A315
• 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:0046677 response to antibiotic

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:2hdq, PDBe:2hdq, PDBj:2hdq
• PDBsum: 2hdq
• PubMed: 17072304
• UniProt: P00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)