Structure of PDB 2xk1 Chain A Binding Site BS01

Receptor Information
>2xk1 Chain A (length=466) Species: 72570 (Actinomadura sp. R39) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASN
MKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSA
EDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQ
ISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTG
AAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFE
EALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNN
GHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLS
RGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRG
TAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQD
AIAVRLAEYAGHQAPE
Ligand information
Ligand IDEWB
InChIInChI=1S/C16H19BNO4/c1-12(17(20,21)22)18-16(19)15-10-6-5-9-14(15)11-13-7-3-2-4-8-13/h2-10,12,20-22H,11H2,1H3,(H,18,19)/q-1/t12-/m1/s1
InChIKeyKXUAFLYMMJHXHZ-GFCCVEGCSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[CH](NC(=O)c1ccccc1Cc2ccccc2)[B-](O)(O)O
ACDLabs 10.04O=C(c1ccccc1Cc2ccccc2)NC([B-](O)(O)O)C
OpenEye OEToolkits 1.6.1[B-]([C@@H](C)NC(=O)c1ccccc1Cc2ccccc2)(O)(O)O
CACTVS 3.352C[C@@H](NC(=O)c1ccccc1Cc2ccccc2)[B-](O)(O)O
OpenEye OEToolkits 1.6.1[B-](C(C)NC(=O)c1ccccc1Cc2ccccc2)(O)(O)O
FormulaC16 H19 B N O4
Name[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-)
ChEMBL
DrugBank
ZINCZINC000198343719
PDB chain2xk1 Chain A Residue 500 [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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PDB2xk1 Structure Guided Development of Potent Reversibly Binding Penicillin Binding Protein Inhibitors
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S49 Y147 S298 N300 L349 G412 T413
Binding residue
(residue number reindexed from 1)		S49 Y147 S298 N300 L349 G412 T413
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.74,IC50=1.8uM
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004185 serine-type carboxypeptidase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2xk1, PDBe:2xk1, PDBj:2xk1
PDBsum2xk1
PubMed24900305
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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