Structure of PDB 6g9f Chain A Binding Site BS01

Receptor Information
>6g9f Chain A (length=539) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRIKLVPIAPSRGIIYDRNGIPLALNRTIYQIEMMPEKVDNVQQTLDALR
SVVDLTDDDIAAFRKERARSHRFTSIPVKTNLTEVQVARFAVNQYRFPGV
EVKGYKRRYYPYGSALTHVIGYVSKINDKDVERLNNDGKLANYAATHDIG
KLGIERYYEDVLHGQTGYEEVEVNNRGRVIRQLKEVPPQAGHDIYLTLDL
KLQQYIETLLAGSRAAVVVTDPRTGGVLALVSTPSYDPNLFVDGISSKDY
SALLNDPNTPLVNRATQGVYPPASTVKPYVAVSALSAGVITRNTTLFDPG
WWQLPGSEKRYRDWKKWGHGRLNVTRSLEESADTFFYQVAYDMGIDRLSE
WMGKFGYGHYTGIDLAEERSGNMPTREWKQKRFKKPWYQGDTIPVGIGQG
YWTATPIQMSKALMILINDGIVKVPHLLMSTAEDGKQVPWVQPHEPPVGD
IHSGYWELAKDGMYGVANRPNGTAHKYFASAPYKIAAKSGTAQLRDHKLM
TAFAPYNNPQVAVAMILENGGAGPAVGTLMRQILDHIML
Ligand information
Ligand IDNXL
InChIInChI=1S/C7H13N3O6S/c8-7(12)6-2-1-5(3-10(6)4-11)9-16-17(13,14)15/h4-6,9H,1-3H2,(H2,8,12)(H,13,14,15)/t5-,6+/m1/s1
InChIKeyWJDGWXPPFHLLNL-RITPCOANSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=CN1C(C(N)=O)CCC(C1)NOS(=O)(O)=O
OpenEye OEToolkits 1.7.6C1CC(N(CC1NOS(=O)(=O)O)C=O)C(=O)N
CACTVS 3.385NC(=O)[CH]1CC[CH](CN1C=O)NO[S](O)(=O)=O
OpenEye OEToolkits 1.7.6C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
CACTVS 3.385NC(=O)[C@@H]1CC[C@H](CN1C=O)NO[S](O)(=O)=O
FormulaC7 H13 N3 O6 S
Name(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide;
avibactam, bound form;
NXL104, bound form
ChEMBL
DrugBank
ZINCZINC000098209247
PDB chain6g9f Chain A Residue 1330 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6g9f Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		S330 W370 S387 D389 S545 G546 T547
Binding residue
(residue number reindexed from 1)		S274 W314 S331 D333 S489 G490 T491
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.23,IC50=0.59uM
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0009252 peptidoglycan biosynthetic process
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6g9f, PDBe:6g9f, PDBj:6g9f
PDBsum6g9f
PubMed30995398
UniProtP0AD65|MRDA_ECOLI Peptidoglycan D,D-transpeptidase MrdA (Gene Name=mrdA)

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