Structure of PDB 1nym Chain A Binding Site BS01

Receptor Information
>1nym Chain A (length=263) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVL
LCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSA
AITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPN
DERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSAL
PAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNR
QIAEIGASLIKHW
Ligand information
Ligand IDCXB
InChIInChI=1S/C7H11BN4O4S/c1-16-12-5(4-2-17-7(9)11-4)6(13)10-3-8(14)15/h2,14-15H,3H2,1H3,(H2,9,11)(H,10,13)/b12-5-
InChIKeyFMYGJTQJYFMFCR-XGICHPGQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0B(CNC(=O)/C(=N\OC)/c1csc(n1)N)(O)O
CACTVS 3.341CO\N=C(/C(=O)NCB(O)O)c1csc(N)n1
ACDLabs 10.04O=C(C(=N\OC)/c1nc(sc1)N)NCB(O)O
OpenEye OEToolkits 1.5.0B(CNC(=O)C(=NOC)c1csc(n1)N)(O)O
CACTVS 3.341CON=C(C(=O)NCB(O)O)c1csc(N)n1
FormulaC7 H11 B N4 O4 S
Name[(2-AMINO-ALPHA-METHOXYIMINO-4-THIAZOLYLACETYL)AMINO]METHYLBORONIC ACID
ChEMBLCHEMBL227452
DrugBankDB07599
ZINCZINC000169748500
PDB chain1nym Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nym Recognition and resistance in TEM beta-lactamase
Resolution1.2 Å
Binding residue
(original residue number in PDB)		S70 K73 Y105 S130 N132 G236 A237 G238 E240
Binding residue
(residue number reindexed from 1)		S45 K48 Y80 S105 N107 G211 A212 G213 E214
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.40,Ki=4.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 A237
Catalytic site (residue number reindexed from 1) S45 K48 S105 E141 K209 A212
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1nym, PDBe:1nym, PDBj:1nym
PDBsum1nym
PubMed12859188
UniProtP62593|BLAT_ECOLX Beta-lactamase TEM (Gene Name=bla)

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