Structure of PDB 8dp2 Chain A Binding Site BS01

Receptor Information
>8dp2 Chain A (length=446) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHHMFRIVVGLGKSGMSLVRYLARRGLPFAVVDTRENPPELATLRAQY
PQVEVRCGELDAEFLCSARELYVSPGLSLRTPALVQAAAKGVRISGDIDL
FAREAKAPIVAITGSNAKSTVTTLVGEMAVAADKRVAVGGNLGTPALDLL
ADDIELYVLELSSFQLETCDRLNAEVATVLNVSEDHMDRYDGMADYHLAK
HRIFRGARQVVVNRADALTRPLIADTVPCWSFGLNKPDFKAFGLIEEDGQ
KWLAFQFDKLLPVGELKIRGAHNYSNALAALALGHAVGLPFDAMLGALKA
FSGLAHRCQWVRERQGVSYYDDSKATNVGAALAAIEGLGADIDGKLVLLA
GGDGKGADFHDLREPVARFCRAVVLLGRDAGLIAQALGNAVPLVRVATLD
EAVRQAAELAREGDAVLLSPACASLDMFKNFEERGRLFAKAVEELA
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 chain8dp2 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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PDB8dp2 Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)
Resolution1.6 Å
Binding residue
(original residue number in PDB)		K17 S18 D37 T38 R39 S76 P77 G78 G142 N143 F166 H188
Binding residue
(residue number reindexed from 1)		K15 S16 D35 T36 R37 S74 P75 G76 G140 N141 F164 H186
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.2.9: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
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

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dp2, PDBe:8dp2, PDBj:8dp2
PDBsum8dp2
PubMed
UniProtQ9HVZ9|MURD_PSEAE UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

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