Structure of PDB 9bn8 Chain A Binding Site BS01

Receptor Information
>9bn8 Chain A (length=438) Species: 83333 (Escherichia coli K-12) [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
VQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELGG
Ligand information
Ligand IDUMA
InChIInChI=1S/C23H36N4O20P2/c1-8(21(35)36)24-19(34)9(2)43-18-14(25-10(3)29)22(45-11(6-28)16(18)32)46-49(40,41)47-48(38,39)42-7-12-15(31)17(33)20(44-12)27-5-4-13(30)26-23(27)37/h4-5,8-9,11-12,14-18,20,22,28,31-33H,6-7H2,1-3H3,(H,24,34)(H,25,29)(H,35,36)(H,38,39)(H,40,41)(H,26,30,37)/t8-,9+,11+,12+,14+,15+,16+,17+,18+,20+,22+/m0/s1
InChIKeyNTMMCWJNQNKACG-KBKUWGQMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)NC(=O)C(C)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
CACTVS 3.341C[CH](NC(=O)[CH](C)O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(O)=O
OpenEye OEToolkits 1.5.0C[C@@H](C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
CACTVS 3.341C[C@H](NC(=O)[C@@H](C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(O)=O
ACDLabs 10.04O=P(OC1OC(C(O)C(OC(C(=O)NC(C(=O)O)C)C)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
FormulaC23 H36 N4 O20 P2
NameURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
ChEMBL
DrugBankDB01673
ZINCZINC000085545647
PDB chain9bn8 Chain A Residue 501 [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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PDB9bn8 Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
Resolution1.35 Å
Binding residue
(original residue number in PDB)		L15 T16 D35 T36 R37 P72 G73 G137 N138 G140 H183
Binding residue
(residue number reindexed from 1)		L15 T16 D35 T36 R37 P72 G73 G137 N138 G140 H183
Annotation score3
Enzymatic activity
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:9bn8, PDBe:9bn8, PDBj:9bn8
PDBsum9bn8
PubMed
UniProtP14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

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