Structure of PDB 1kds Chain A Binding Site BS01

Receptor Information
>1kds Chain A (length=358) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQP
VTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNG
ITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANS
SIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGY
REGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQ
LAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITP
PTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAA
WQILNALQ
Ligand information
Ligand IDNPB
InChIInChI=1S/C6H6BNO4/c9-7(10)5-2-1-3-6(4-5)8(11)12/h1-4,9-10H
InChIKeyZNRGSYUVFVNSAW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04[O-][N+](=O)c1cc(B(O)O)ccc1
CACTVS 3.341OB(O)c1cccc(c1)[N+]([O-])=O
OpenEye OEToolkits 1.5.0B(c1cccc(c1)[N+](=O)[O-])(O)O
FormulaC6 H6 B N O4
Name3-NITROPHENYLBORONIC ACID
ChEMBLCHEMBL20945
DrugBankDB02797
ZINCZINC000169743203
PDB chain1kds Chain A Residue 364 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kds Structure-based approach for binding site identification on AmpC beta-lactamase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		S64 Y150 N152 Y221 G317 A318
Binding residue
(residue number reindexed from 1)		S61 Y147 N149 Y218 G314 A315
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.77,Ki=1.7uM
BindingDB: Ki=1700nM,IC50=5000nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kds, PDBe:1kds, PDBj:1kds
PDBsum1kds
PubMed12109906
UniProtP00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)

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