Structure of PDB 2wjp Chain A Binding Site BS01

Receptor Information
>2wjp Chain A (length=435) Species: 668369 (Escherichia coli DH5[alpha]) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAV
ERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCR
EAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDE
CELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLR
IYENAKVCVVNADDALTMPIRRCVSFGVNMGDYHLNHQQGETWLRVKGEK
VLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFE
VVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSP
LARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPG
DMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH
Ligand information
Ligand IDD17
InChIInChI=1S/C23H21N3O6S2/c27-19(28)9-8-17(22(31)32)25-20(29)15-3-1-2-14(10-15)12-24-16-6-4-13(5-7-16)11-18-21(30)26-23(33)34-18/h1-7,10-11,17,24H,8-9,12H2,(H,25,29)(H,27,28)(H,31,32)(H,26,30,33)/b18-11-/t17-/m0/s1
InChIKeyISIOCNFLEMFKTN-PBXDPIQXSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1C(\SC(=S)N1)=C\c3ccc(NCc2cc(C(=O)NC(C(=O)O)CCC(=O)O)ccc2)cc3
OpenEye OEToolkits 1.6.1c1cc(cc(c1)C(=O)NC(CCC(=O)O)C(=O)O)CNc2ccc(cc2)C=C3C(=O)NC(=S)S3
CACTVS 3.352OC(=O)CC[C@H](NC(=O)c1cccc(CNc2ccc(cc2)\C=C3/SC(=S)NC3=O)c1)C(O)=O
OpenEye OEToolkits 1.6.1c1cc(cc(c1)C(=O)N[C@@H](CCC(=O)O)C(=O)O)CNc2ccc(cc2)\C=C/3\C(=O)NC(=S)S3
CACTVS 3.352OC(=O)CC[CH](NC(=O)c1cccc(CNc2ccc(cc2)C=C3SC(=S)NC3=O)c1)C(O)=O
FormulaC23 H21 N3 O6 S2
NameN-({3-[({4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-L-glutamic acid
ChEMBL
DrugBank
ZINCZINC000058661048
PDB chain2wjp Chain A Residue 1441 [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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PDB2wjp Discovery of Novel 5-Benzylidenerhodanine and 5-Benzylidenethiazolidine-2,4-Dione Inhibitors of Murd Ligase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		D35 T36 R37 S71 G73 F161 H183 K348 A414 S415 L416 N421 F422
Binding residue
(residue number reindexed from 1)		D35 T36 R37 S71 G73 F161 H183 K344 A410 S411 L412 N417 F418
Annotation score1
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2wjp, PDBe:2wjp, PDBj:2wjp
PDBsum2wjp
PubMed20804196
UniProtP14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

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