Structure of PDB 4nk3 Chain A Binding Site BS01

Receptor Information
>4nk3 Chain A (length=361) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGR
RVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFD
GISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYS
NPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQ
GYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQA
LDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARL
PAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVK
IAYAILSGLEQ
Ligand information
Ligand IDMK7
InChIInChI=1S/C12H22N4O6S/c17-8-16-7-10(15-22-23(19,20)21)1-2-11(16)12(18)14-9-3-5-13-6-4-9/h8-11,13,15H,1-7H2,(H,14,18)(H,19,20,21)/t10-,11+/m1/s1
InChIKeyVGHMECNLFQGIJM-MNOVXSKESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NC2CCNCC2
CACTVS 3.385O[S](=O)(=O)ON[CH]1CC[CH](N(C1)C=O)C(=O)NC2CCNCC2
ACDLabs 12.01O=CN2C(C(=O)NC1CCNCC1)CCC(NOS(=O)(=O)O)C2
CACTVS 3.385O[S](=O)(=O)ON[C@@H]1CC[C@H](N(C1)C=O)C(=O)NC2CCNCC2
OpenEye OEToolkits 1.7.6C1CC(N(CC1NOS(=O)(=O)O)C=O)C(=O)NC2CCNCC2
FormulaC12 H22 N4 O6 S
Name(2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide;
MK-7655, bound form
ChEMBL
DrugBank
ZINCZINC000098209180
PDB chain4nk3 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nk3 Discovery of MK-7655, a beta-lactamase inhibitor for combination with Primaxin().
Resolution1.9 Å
Binding residue
(original residue number in PDB)
S90 Q146 Y177 N179 Y249 T343 G344 S345 N347
Binding residue
(residue number reindexed from 1)
S62 Q118 Y149 N151 Y221 T315 G316 S317 N319
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.33,IC50=465nM
Enzymatic activity
Catalytic site (original residue number in PDB) S90 K93 Y177 E299 K342 S345
Catalytic site (residue number reindexed from 1) S62 K65 Y149 E271 K314 S317
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:4nk3, PDBe:4nk3, PDBj:4nk3
PDBsum4nk3
PubMed24433862
UniProtP24735|AMPC_PSEAE Beta-lactamase (Gene Name=ampC)

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