Structure of PDB 1mpl Chain A Binding Site BS01

Receptor Information
>1mpl Chain A (length=345) Species: 31952 (Streptomyces sp. R61) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAI
TTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITV
RQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNA
PGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPD
TVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFS
ALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTV
QGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKP
Ligand information
Ligand IDRE1
InChIInChI=1S/C11H22N3O7P/c1-7(22(19,20)21)13-9(15)5-3-2-4-8(11(17)18)14-10(16)6-12/h7-8H,2-6,12H2,1H3,(H,13,15)(H,14,16)(H,17,18)(H2,19,20,21)/p-1/t7-,8-/m0/s1
InChIKeyDREJXTKPUGMERN-YUMQZZPRSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(NC(=O)CCCCC(C(=O)[O-])NC(=O)C[NH3+])P(=O)(O)[O-]
CACTVS 3.341C[CH](NC(=O)CCCC[CH](NC(=O)C[NH3+])C([O-])=O)[P](O)([O-])=O
ACDLabs 10.04[O-]P(=O)(O)C(NC(=O)CCCCC(C([O-])=O)NC(=O)C[NH3+])C
OpenEye OEToolkits 1.5.0C[C@@H](NC(=O)CCCC[C@@H](C(=O)[O-])NC(=O)C[NH3+])[P@](=O)(O)[O-]
CACTVS 3.341C[C@@H](NC(=O)CCCC[C@H](NC(=O)C[NH3+])C([O-])=O)[P](O)([O-])=O
FormulaC11 H21 N3 O7 P
NameGLYCYL-L-A-AMINOPIMELYL-E-(D-2-AMINOETHYL)PHOSPHONATE
ChEMBL
DrugBankDB01868
ZINC
PDB chain1mpl 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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PDB1mpl The Crystal Structure of Phosphonate-Inhibited d-Ala-d-Ala Peptidase Reveals an Analogue of a Tetrahedral Transition State.
Resolution1.12 Å
Binding residue
(original residue number in PDB)		S62 F120 T123 Y159 N161 W233 G300 T301 Q303 S326 N327
Binding residue
(residue number reindexed from 1)		S60 F118 T121 Y157 N159 W231 G298 T299 Q301 S324 N325
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.77,Ki=0.17mM
Enzymatic activity
Catalytic site (original residue number in PDB) S62 K65 D114 T116 V130 Y159 N161 V165 T227 H298 G304
Catalytic site (residue number reindexed from 1) S60 K63 D112 T114 V128 Y157 N159 V163 T225 H296 G302
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
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:1mpl, PDBe:1mpl, PDBj:1mpl
PDBsum1mpl
PubMed12564922
UniProtP15555|DAC_STRSR D-alanyl-D-alanine carboxypeptidase

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