Structure of PDB 2exb Chain A Binding Site BS01

Receptor Information
>2exb Chain A (length=446) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEYITQLPAGANLALMVQKVGASAPAIDYHSQQMALPASTQKVITALAAL
IQLGPDFRFTTTLETKGNVENGVLKGDLVARFGADPTLKRQDIRNMVATL
KKSGVNQIDGNVLIDTSIFASHDKAPGWPWNDMTQCFSAPPAAAIVDRNC
FSVSLYSAPKPGDMAFIRVASYYPVTMFSQVRTLPRGSAEAQYCELDVVP
GDLNRFTLTGCLPQRSEPLPLAFAVQDGASYAGAILKYELKQAGITWSGT
LLRQTQVNEPGTVVASKQSAPLHDLLKIMLKKSDNMIADTVFRMIGHARF
NVPGTWRAGSDAVRQILRQQAGVDIGNTIIADGSGLSRHNLIAPATMMQV
LQYIAQHDNELNFISMLPLAGYDGSLQYRAGLHQAGVDGKVSAKTGSLQG
VYNLAGFITTASGQRMAFVQYLSGYAVRIPLVRFESRLYKDIYQNN
Ligand information
Ligand IDFXM
InChIInChI=1S/C23H31N5O8S2/c1-5-6-13(15-10-38-21(24)27-15)17(30)26-14(7-29)18-28-16(12(9-37-18)8-34-22(25)33)19(31)35-11-36-20(32)23(2,3)4/h6-7,10,14,18,28H,5,8-9,11H2,1-4H3,(H2,24,27)(H2,25,33)(H,26,30)/b13-6-/t14-,18-/m1/s1
InChIKeyCXZSGDIZUNIAQH-FJWVKOTRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC/C=C(/c1csc(n1)N)\C(=O)N[C@H](C=O)[C@@H]2NC(=C(CS2)COC(=O)N)C(=O)OCOC(=O)C(C)(C)C
CACTVS 3.385CCC=C(C(=O)N[CH](C=O)[CH]1NC(=C(COC(N)=O)CS1)C(=O)OCOC(=O)C(C)(C)C)c2csc(N)n2
OpenEye OEToolkits 1.7.6CCC=C(c1csc(n1)N)C(=O)NC(C=O)C2NC(=C(CS2)COC(=O)N)C(=O)OCOC(=O)C(C)(C)C
CACTVS 3.385CC\C=C(/C(=O)N[C@H](C=O)[C@@H]1NC(=C(COC(N)=O)CS1)C(=O)OCOC(=O)C(C)(C)C)c2csc(N)n2
FormulaC23 H31 N5 O8 S2
Name2,2-dimethylpropanoyloxymethyl (2R)-5-(aminocarbonyloxymethyl)-2-[(1R)-1-[[(Z)-2-(2-azanyl-1,3-thiazol-4-yl)pent-2-enoyl]amino]-2-oxidanylidene-ethyl]- 3,6-dihydro-2H-1,3-thiazine-4-carboxylate;
FLOMOX open form
ChEMBL
DrugBank
ZINCZINC000584905577
PDB chain2exb Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2exb Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics
Resolution1.75 Å
Binding residue
(original residue number in PDB)		S62 F160 S306 G358 L359 R361 S420 L421
Binding residue
(residue number reindexed from 1)		S39 F137 S283 G335 L336 R338 S397 L398
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
3.4.21.-
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004180 carboxypeptidase activity
GO:0004185 serine-type carboxypeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0043093 FtsZ-dependent cytokinesis
GO:0046677 response to antibiotic
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2exb, PDBe:2exb, PDBj:2exb
PDBsum2exb
PubMed16411754
UniProtP24228|DACB_ECOLI D-alanyl-D-alanine carboxypeptidase DacB (Gene Name=dacB)

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