Structure of PDB 2xdm Chain B Binding Site BS01

Receptor Information
>2xdm Chain B (length=465) 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
AIAVRLAEYAGHQAP
Ligand information
Ligand IDBO8
InChIInChI=1S/C9H20BN2O6/c1-6(10(16,17)18)12-8(13)5-3-2-4-7(11)9(14)15/h6-7,16-18H,2-5,11H2,1H3,(H,12,13)(H,14,15)/q-1/t6-,7-/m1/s1
InChIKeyZSMKWHGOAVMEJJ-RNFRBKRXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1[B-]([C@@H](C)NC(=O)CCCC[C@H](C(=O)O)N)(O)(O)O
ACDLabs 10.04O=C(NC(C)[B-](O)(O)O)CCCCC(C(=O)O)N
CACTVS 3.352C[C@@H](NC(=O)CCCC[C@@H](N)C(O)=O)[B-](O)(O)O
CACTVS 3.352C[CH](NC(=O)CCCC[CH](N)C(O)=O)[B-](O)(O)O
OpenEye OEToolkits 1.6.1[B-](C(C)NC(=O)CCCCC(C(=O)O)N)(O)(O)O
FormulaC9 H20 B N2 O6
Name(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONIC ACID
ChEMBL
DrugBank
ZINCZINC000198004839
PDB chain2xdm Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xdm Crystal Structure of a Complex between the Actinomadura R39 Dd-Peptidase and a Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		S49 W139 D142 Y147 S298 N300 L349 G412 T413 M414 S415
Binding residue
(residue number reindexed from 1)		S49 W139 D142 Y147 S298 N300 L349 G412 T413 M414 S415
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.49,Ki=32nM
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:2xdm, PDBe:2xdm, PDBj:2xdm
PDBsum2xdm
PubMed20608745
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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