Structure of PDB 5hld Chain A Binding Site BS01

Receptor Information
>5hld Chain A (length=649) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIVFAVLIAIYGVYLDQKIRSRIDGKVWQLPAAVYGRMVNLEPDMTISKN
EMVKLLEATQYRQVSKMTRPGEFTVQANSIEMIRRPFDFPDSKEGQVRAR
LTFDGDHLATIVNMENNRQFGFFRLDPRLITMISSPNGEQRLFVPRSGFP
DLLVDTLLATETQQLVKNLFLSKANEAYMALIMDARYSKDRILELYMNEV
YLGQSGDNEIRGFPLASLYYFGRPVEELSLDQQALLVGMVLALERRNLVL
RLLYDMLSARPQPAFMQLVRQELQAKLGDKVKDLSGVKIFTTFDSVAQDA
AEKAAVEGIPALKKQRKLSDLETAIVVVDRFSGEVRAMVGGSEPQFAGYN
RAMQARRSIGSLAKPATYLTALSQPKIYRLNTWIADAPIALRQPNGQVWS
PQNDDRRYSESGRVMLVDALTRSMNVPTVNLGMALGLPAVTETWIKLGVP
KDQLHPVPAMLLGALNLTPIEVAQAFQTIASGGNRAPLSALRSVIAEDGK
VLYQSFPQAERAVPAQAAYLTLWTMQQVVQRGTGRQLGAKYPNLHLAGKT
GTTNNNVDTWFAGIDGSTVTITWVGRDNNQPTKLYGASGAMSIYQRYLAN
QTPTPLNLVPPEDIADMGVDYDGNFVCSGGMRILPVWTSDPQSLCQQSE
Ligand information
Ligand ID63V
InChIInChI=1S/C14H14N2O4S2/c1-8-7-22-13(16-12(8)14(19)20)10(6-17)15-11(18)5-9-3-2-4-21-9/h2-4,6,10,13H,1,5,7H2,(H,15,18)(H,19,20)/t10-,13+/m1/s1
InChIKeyFYGLCWWPHIWVKN-MFKMUULPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4C=C1CSC(N=C1C(=O)O)C(C=O)NC(=O)Cc2cccs2
OpenEye OEToolkits 2.0.4C=C1CS[C@H](N=C1C(=O)O)[C@@H](C=O)NC(=O)Cc2cccs2
CACTVS 3.385OC(=O)C1=N[CH](SCC1=C)[CH](NC(=O)Cc2sccc2)C=O
CACTVS 3.385OC(=O)C1=N[C@@H](SCC1=C)[C@H](NC(=O)Cc2sccc2)C=O
ACDLabs 12.01O=C(C\1=NC(SCC/1=C)C(C=O)NC(=O)Cc2sccc2)O
FormulaC14 H14 N2 O4 S2
Name(2S)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000034932135
PDB chain5hld Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5hld Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition.
Resolution2.31 Å
Binding residue
(original residue number in PDB)
S510 D553 N574 T699 T701 T702 N703
Binding residue
(residue number reindexed from 1)
S361 D404 N425 T550 T552 T553 N554
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.66,IC50=22uM
Enzymatic activity
Enzyme Commision number 2.4.99.28: peptidoglycan glycosyltransferase.
3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
GO:0008658 penicillin binding
GO:0008955 peptidoglycan glycosyltransferase activity
Biological Process
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
Cellular Component
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5hld, PDBe:5hld, PDBj:5hld
PDBsum5hld
PubMed27899450
UniProtP02919|PBPB_ECOLI Penicillin-binding protein 1B (Gene Name=mrcB)

[Back to BioLiP]