Structure of PDB 5j8x Chain A Binding Site BS01

Receptor Information
>5j8x Chain A (length=340) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYV
IGQAMKAGKFKETDLVTIGNMFLKPGMQVPVSQLIRGINLQSGNDACVAM
ADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALI
GQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTD
KAGYNLVASATEGQMRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNP
LKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSE
LHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEGNFF
Ligand information
Ligand IDOK3
InChIInChI=1S/C17H18BN2O6/c19-9-10-4-6-11(7-5-10)16(21)20-14-8-12-2-1-3-13(17(22)23)15(12)26-18(14,24)25/h1-7,14,24-25H,8-9,19H2,(H,20,21)(H,22,23)/q-1/t14-/m0/s1
InChIKeyQLXKUYDHLJOWQG-AWEZNQCLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCc1ccc(cc1)C(=O)N[C@H]2Cc3cccc(C(O)=O)c3O[B-]2(O)O
OpenEye OEToolkits 2.0.7[B-]1(C(Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3)CN)(O)O
OpenEye OEToolkits 2.0.7[B-]1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3)CN)(O)O
CACTVS 3.385NCc1ccc(cc1)C(=O)N[CH]2Cc3cccc(C(O)=O)c3O[B-]2(O)O
FormulaC17 H18 B N2 O6
Name(4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid
ChEMBLCHEMBL4461260
DrugBank
ZINC
PDB chain5j8x Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5j8x Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.
Resolution2.53 Å
Binding residue
(original residue number in PDB)		S44 S110 L153 R198 T214 G215 H216 D218 R248
Binding residue
(residue number reindexed from 1)		S41 S92 L135 R180 T196 G197 H198 D200 R230
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.80,IC50=0.0016uM
Enzymatic activity
Catalytic site (original residue number in PDB) L22 G28 L45 M48 M49 T50
Catalytic site (residue number reindexed from 1) L19 G25 L42 M45 M46 T47
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008658 penicillin binding
GO:0008800 beta-lactamase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0030288 outer membrane-bounded periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5j8x, PDBe:5j8x, PDBj:5j8x
PDBsum5j8x
PubMed27499424
UniProtP0AEB2|DACA_ECOLI D-alanyl-D-alanine carboxypeptidase DacA (Gene Name=dacA)

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