Structure of PDB 6g9s Chain A Binding Site BS01

Receptor Information
>6g9s Chain A (length=538) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRIKLVPIAPSRGIIYDRNGIPLALNRTIYQIEMMPEKVDNVQQTLDALR
SVVDLTDDDIAAFRKERARSHRFTSIPVKTNLTEVQVARFAVNQYRFPGV
EVKGYKRRYYPYGSALTHVIGYVSKINDKDVERLNNDGKLANYAATHDIG
KLGIERYYEDVLHGQTGYEEVEVNNRGRVIRQLKEVPPQAGHDIYLTLDL
KLQQYIETLLAGSRAAVVVTDPRTGGVLALVSTPSYDPNLFVDGISSKDY
SALLNDPNTPLVNRATQGVYPPASTVKPYVAVSALSAGVITRNTTLFDPG
WWQLPGSEKRYRDWKKWGHGRLNVTRSLEESADTFFYQVAYDMGIDRLSE
WMGKFGYGHYTGIDLAEERSGNMPTREWKQKRFKKPWYQGDTIPVGIGQG
YWTATPIQMSKALMILINDGIVKVPHLLMSTAEDGKQVPWVQPHEPPVGD
IHSGYWELAKDGMYGVANRPNGTAHKYFASAPYKIAAKSGTAQRDHKLMT
AFAPYNNPQVAVAMILENGGAGPAVGTLMRQILDHIML
Ligand information
Ligand IDET5
InChIInChI=1S/C10H14N4O7S/c11-2-6-1-7(9-3-12-5-20-9)8(4-14(6)10(15)16)13-21-22(17,18)19/h1,3,5-6,8,13H,2,4,11H2,(H,15,16)(H,17,18,19)/t6-,8-/m0/s1
InChIKeyABKLGTMGWHFUKR-XPUUQOCRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC[CH]1C=C([CH](CN1C(O)=O)NO[S](O)(=O)=O)c2ocnc2
OpenEye OEToolkits 2.0.6c1c(ocn1)C2=CC(N(CC2NOS(=O)(=O)O)C(=O)O)CN
OpenEye OEToolkits 2.0.6c1c(ocn1)C2=C[C@H](N(C[C@@H]2NOS(=O)(=O)O)C(=O)O)CN
CACTVS 3.385NC[C@@H]1C=C([C@H](CN1C(O)=O)NO[S](O)(=O)=O)c2ocnc2
FormulaC10 H14 N4 O7 S
Name(3~{R},6~{S})-6-(aminomethyl)-4-(1,3-oxazol-5-yl)-3-(sulfooxyamino)-3,6-dihydro-2~{H}-pyridine-1-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6g9s Chain A Residue 701 [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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PDB6g9s Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.
Resolution2.001 Å
Binding residue
(original residue number in PDB)
S330 W370 S387 D389 S545 G546 T547
Binding residue
(residue number reindexed from 1)
S274 W314 S331 D333 S489 G490 T491
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.00,IC50=0.01uM
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:0005515 protein binding
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0071972 peptidoglycan L,D-transpeptidase activity
Biological 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:0005886 plasma membrane
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6g9s, PDBe:6g9s, PDBj:6g9s
PDBsum6g9s
PubMed30995398
UniProtP0AD65|MRDA_ECOLI Peptidoglycan D,D-transpeptidase MrdA (Gene Name=mrdA)

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