Structure of PDB 2y67 Chain A Binding Site BS01

Receptor Information

>2y67 Chain A (length=435) Species: 83333 (Escherichia coli K-12)

ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAV
ERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCR
EAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDE
CELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLR
IYENAKVCVVNADDALTMPIERCVSFGVNMGDYHLNHQQGETWLRVKGEK
VLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFE
VVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSP
LARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPG
DMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH

Ligand information

• Ligand ID: N21
• InChI: InChI=1S/C22H20N2O9S2/c25-19(26)10-9-17(21(28)29)24-35(31,32)16-7-3-14(4-8-16)12-33-15-5-1-13(2-6-15)11-18-20(27)23-22(30)34-18/h1-8,11,17,24H,9-10,12H2,(H,25,26)(H,28,29)(H,23,27,30)/b18-11-/t17-/m1/s1
• InChIKey: BZCXCLVFYJNKLW-LVSMMTLPSA-N
• SMILES:
  CACTVS 3.352: OC(=O)CC[CH](N[S](=O)(=O)c1ccc(COc2ccc(cc2)C=C3SC(=O)NC3=O)cc1)C(O)=O
  CACTVS 3.352: OC(=O)CC[C@@H](N[S](=O)(=O)c1ccc(COc2ccc(cc2)\C=C3/SC(=O)NC3=O)cc1)C(O)=O
  OpenEye OEToolkits 1.6.1: c1cc(ccc1COc2ccc(cc2)C=C3C(=O)NC(=O)S3)S(=O)(=O)NC(CCC(=O)O)C(=O)O
  OpenEye OEToolkits 1.6.1: c1cc(ccc1COc2ccc(cc2)\C=C/3\C(=O)NC(=O)S3)S(=O)(=O)N[C@H](CCC(=O)O)C(=O)O
• Formula: C22 H20 N2 O9 S2
• Name: (2R)-2-[[4-[[4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]methyl]phenyl]sulfonylamino]pentanedioic acid
• ChEMBL: CHEMBL1928360
• ZINC: ZINC000073220732
• PDB chain: 2y67 Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2y67 New 5-Benzylidenethiazolidin-4-One Inhibitors of Bacterial Murd Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): D35 T36 R37 S71 F161 H183 K348 A414 S415 N421 F422
• Binding residue (residue number reindexed from 1): D35 T36 R37 S71 F161 H183 K344 A410 S411 N417 F418
• Annotation score: 1
• Binding affinity: MOAD: ic50=292uM
  PDBbind-CN: -logKd/Ki=3.53,IC50=292uM

Enzymatic activity

• Catalytic site (original residue number in PDB): K115 S116 N138 L147 H183
• Catalytic site (residue number reindexed from 1): K115 S116 N138 L147 H183
• Enzyme Commision number: 6.3.2.9: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase.

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
• GO:0016874 ligase activity
• GO:0016881 acid-amino acid ligase activity
• GO:0042802 identical protein binding

Biological Process

• GO:0008360 regulation of cell shape
• GO:0009058 biosynthetic process
• GO:0009252 peptidoglycan biosynthetic process
• GO:0051301 cell division
• GO:0071555 cell wall organization

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2y67, PDBe:2y67, PDBj:2y67
• PDBsum: 2y67
• PubMed: 21963114
• UniProt: P14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)