Structure of PDB 3nck Chain A Binding Site BS01

Receptor Information
>3nck Chain A (length=256) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLADRFAELERRYDARLGVYVPATGTTAAIEYRADERFAFCSTFKAPLVA
AVLHQNPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYS
DGTAANLLLADLGGPGGGTAAFTGYLRSLGDTVSRLDPPGDERDTTTPHA
IALVLQQLVLGNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKT
GTGDYGRANDIAVVWSPTGVPYVVAVMSDRAGGGYDAEPREALLAEAATC
VAGVLA
Ligand information
Ligand IDNFF
InChIInChI=1S/C21H24N2O5S/c1-4-28-15-10-9-12-7-5-6-8-13(12)16(15)18(25)22-14(11-24)19-23-17(20(26)27)21(2,3)29-19/h5-11,14,17,19,23H,4H2,1-3H3,(H,22,25)(H,26,27)/t14-,17+,19-/m1/s1
InChIKeyXDLYHUOUOKHAMD-DKSSEZFCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCOc1ccc2ccccc2c1C(=O)NC(C=O)C3NC(C(S3)(C)C)C(=O)O
ACDLabs 12.01O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)c3c2ccccc2ccc3OCC
OpenEye OEToolkits 1.7.6CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@H](C(S3)(C)C)C(=O)O
CACTVS 3.370CCOc1ccc2ccccc2c1C(=O)N[CH](C=O)[CH]3N[CH](C(O)=O)C(C)(C)S3
CACTVS 3.370CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@@H](C(O)=O)C(C)(C)S3
FormulaC21 H24 N2 O5 S
Name(2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
Nafcillin, bound form
ChEMBL
DrugBank
ZINCZINC000095921260
PDB chain3nck Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nck BlaC-E166A covalently bound with cephalosporins and penicillins
Resolution2.8 Å
Binding residue
(original residue number in PDB)
S84 I117 S142 T251 G252 T253 G254 D255
Binding residue
(residue number reindexed from 1)
S42 I75 S100 T200 G201 T202 G203 D204
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S84 K87 S142 K250 T253
Catalytic site (residue number reindexed from 1) S42 K45 S100 K199 T202
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
Cellular Component
GO:0005576 extracellular region
GO:0005886 plasma membrane
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:3nck, PDBe:3nck, PDBj:3nck
PDBsum3nck
PubMed
UniProtP9WKD3|BLAC_MYCTU Beta-lactamase (Gene Name=blaC)

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