Structure of PDB 4r5m Chain A Binding Site BS02

Receptor Information
>4r5m Chain A (length=369) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDA
GMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTL
RMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERG
LVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDID
KKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANK
ILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHND
WVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQ
LLWGAAEPLRRTLRIILAE
Ligand information
Ligand ID4NO
InChIInChI=1S/C7H6NO7P/c9-7(10)5-2-1-4(8(11)12)3-6(5)16(13,14)15/h1-3H,(H,9,10)(H2,13,14,15)
InChIKeyPFWUFGANONPVGT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)c1ccc(cc1[P](O)(O)=O)[N+]([O-])=O
OpenEye OEToolkits 1.7.6c1cc(c(cc1[N+](=O)[O-])P(=O)(O)O)C(=O)O
ACDLabs 12.01[O-][N+](=O)c1cc(c(C(=O)O)cc1)P(=O)(O)O
FormulaC7 H6 N O7 P
Name4-nitro-2-phosphonobenzoic acid
ChEMBL
DrugBank
ZINCZINC000001870296
PDB chain4r5m Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r5m A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		C71 G73 G74 A96 A97 S98 R101 K243
Binding residue
(residue number reindexed from 1)		C71 G73 G74 A96 A97 S98 R101 K243
Annotation score1
Binding affinityMOAD: Ki=0.076mM
Enzymatic activity
Catalytic site (original residue number in PDB) C134 Q161 R267 H274
Catalytic site (residue number reindexed from 1) C134 Q161 R267 H274
Enzyme Commision number 1.2.1.11: aspartate-semialdehyde dehydrogenase.
Gene Ontology
Molecular Function
GO:0004073 aspartate-semialdehyde dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0046983 protein dimerization activity
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0008652 amino acid biosynthetic process
GO:0009085 lysine biosynthetic process
GO:0009086 methionine biosynthetic process
GO:0009088 threonine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0009097 isoleucine biosynthetic process
GO:0019877 diaminopimelate biosynthetic process
GO:0071266 'de novo' L-methionine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4r5m, PDBe:4r5m, PDBj:4r5m
PDBsum4r5m
PubMed25478842
UniProtQ9KQG2|DHAS1_VIBCH Aspartate-semialdehyde dehydrogenase 1 (Gene Name=asd1)

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