Structure of PDB 3zcz Chain B Binding Site BS01

Receptor Information
>3zcz 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 IDTFR
InChIInChI=1S/C11H19F3N2O4/c1-6(9(18)11(12,13)14)16-8(17)5-3-2-4-7(15)10(19)20/h6-7,9,18H,2-5,15H2,1H3,(H,16,17)(H,19,20)/t6-,7-,9+/m1/s1
InChIKeyGCYIIHHJPYOBBJ-BHNWBGBOSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)C(O)C(NC(=O)CCCCC(C(=O)O)N)C
CACTVS 3.370C[CH](NC(=O)CCCC[CH](N)C(O)=O)[CH](O)C(F)(F)F
CACTVS 3.370C[C@@H](NC(=O)CCCC[C@@H](N)C(O)=O)[C@H](O)C(F)(F)F
OpenEye OEToolkits 1.7.6CC(C(C(F)(F)F)O)NC(=O)CCCCC(C(=O)O)N
OpenEye OEToolkits 1.7.6C[C@H]([C@@H](C(F)(F)F)O)NC(=O)CCCC[C@H](C(=O)O)N
FormulaC11 H19 F3 N2 O4
Name(2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid
ChEMBL
DrugBank
ZINCZINC000095920560
PDB chain3zcz 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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PDB3zcz Inhibition of Dd-Peptidases by a Specific Trifluoroketone: Crystal Structure of a Complex with the Actinomadura R39 Dd-Peptidase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S49 W139 D142 Y147 S298 N300 G412 T413 M414 S415
Binding residue
(residue number reindexed from 1)		S49 W139 D142 Y147 S298 N300 G412 T413 M414 S415
Annotation score1
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:3zcz, PDBe:3zcz, PDBj:3zcz
PDBsum3zcz
PubMed23484909
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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