Structure of PDB 2r9x Chain B Binding Site BS01

Receptor Information
>2r9x Chain B (length=358) Species: 83333 (Escherichia coli K-12) [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 IDWH6
InChIInChI=1S/C23H17NO6/c25-20(26)12-16(10-14-6-3-5-13-4-1-2-7-17(13)14)24-21(27)18-9-8-15(23(29)30)11-19(18)22(24)28/h1-9,11,16H,10,12H2,(H,25,26)(H,29,30)/t16-/m1/s1
InChIKeyGPOKTQCDBPECSS-MRXNPFEDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2c(c1)cccc2C[C@H](CC(=O)O)N3C(=O)c4ccc(cc4C3=O)C(=O)O
CACTVS 3.341OC(=O)C[CH](Cc1cccc2ccccc12)N3C(=O)c4ccc(cc4C3=O)C(O)=O
ACDLabs 10.04O=C(O)CC(N2C(=O)c1ccc(cc1C2=O)C(=O)O)Cc4c3ccccc3ccc4
OpenEye OEToolkits 1.5.0c1ccc2c(c1)cccc2CC(CC(=O)O)N3C(=O)c4ccc(cc4C3=O)C(=O)O
CACTVS 3.341OC(=O)C[C@@H](Cc1cccc2ccccc12)N3C(=O)c4ccc(cc4C3=O)C(O)=O
FormulaC23 H17 N O6
Name2-[(1R)-2-carboxy-1-(naphthalen-1-ylmethyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid
ChEMBL
DrugBankDB08731
ZINCZINC000016052515
PDB chain2r9x Chain B Residue 365 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2r9x Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S64 Q120 V211 Y221 G317 A318 T319 G320
Binding residue
(residue number reindexed from 1)		S61 Q117 V208 Y218 G314 A315 T316 G317
Annotation score1
Binding affinityMOAD: Ki=14uM
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:2r9x, PDBe:2r9x, PDBj:2r9x
PDBsum2r9x
PubMed18333608
UniProtP00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)

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