Structure of PDB 4wm9 Chain A Binding Site BS01

Receptor Information
>4wm9 Chain A (length=243) Species: 470 (Acinetobacter baumannii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPA
STFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAV
PVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEV
NFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGPQVGWL
TGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII
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 chain4wm9 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4wm9 Molecular Basis of Selective Inhibition and Slow Reversibility of Avibactam against Class D Carbapenemases: A Structure-Guided Study of OXA-24 and OXA-48.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
S81 W115 S128 L168 S219 G220 W221 M223 R261
Binding residue
(residue number reindexed from 1)
S51 W85 S98 L138 S189 G190 W191 M193 R229
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.92,Kd=0.12uM
Enzymatic activity
Catalytic site (original residue number in PDB) S81 K84 S128 Y133 W167 W221
Catalytic site (residue number reindexed from 1) S51 K54 S98 Y103 W137 W191
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008658 penicillin binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
Biological Process
GO:0071555 cell wall organization

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4wm9, PDBe:4wm9, PDBj:4wm9
PDBsum4wm9
PubMed25406838
UniProtQ8RLA6

[Back to BioLiP]