Structure of PDB 2x5o Chain A Binding Site BS01

Receptor Information
>2x5o Chain A (length=439) 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
IYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRV
KGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLP
HRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSA
DFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPR
VQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH
Ligand information
Ligand IDVSV
InChIInChI=1S/C23H21N3O7S/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-/m1/s1
InChIKeyYITBSJALJWUAQA-LVSMMTLPSA-N
SMILES
SoftwareSMILES
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(=O)S3
OpenEye OEToolkits 1.6.1c1cc(cc(c1)C(=O)NC(CCC(=O)O)C(=O)O)CNc2ccc(cc2)C=C3C(=O)NC(=O)S3
CACTVS 3.352OC(=O)CC[C@@H](NC(=O)c1cccc(CNc2ccc(cc2)\C=C3/SC(=O)NC3=O)c1)C(O)=O
ACDLabs 10.04O=C1C(\SC(=O)N1)=C\c3ccc(NCc2cc(C(=O)NC(C(=O)O)CCC(=O)O)ccc2)cc3
CACTVS 3.352OC(=O)CC[CH](NC(=O)c1cccc(CNc2ccc(cc2)C=C3SC(=O)NC3=O)c1)C(O)=O
FormulaC23 H21 N3 O7 S
NameN-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-D-GLUTAMIC ACID
ChEMBLCHEMBL1236691
DrugBank
ZINCZINC000058655684
PDB chain2x5o Chain A Residue 500 [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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PDB2x5o Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase.
Resolution1.46 Å
Binding residue
(original residue number in PDB)		D35 T36 R37 S71 P72 G73 F161 H183 K348 A414 S415 L416 N421 F422
Binding residue
(residue number reindexed from 1)		D35 T36 R37 S71 P72 G73 F161 H183 K348 A414 S415 L416 N421 F422
Annotation score1
Binding affinityMOAD: ic50=85uM
PDBbind-CN: -logKd/Ki=4.07,IC50=85uM
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:2x5o, PDBe:2x5o, PDBj:2x5o
PDBsum2x5o
PubMed20804196
UniProtP14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

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