Structure of PDB 4r3n Chain B Binding Site BS03

Receptor Information
>4r3n Chain B (length=347) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQD
ITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQN
PDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIV
STYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPI
AFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSA
HSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRD
TFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVR
Ligand information
Ligand ID3GQ
InChIInChI=1S/C9H6O6/c10-7(11)4-2-1-3-5(8(12)13)6(4)9(14)15/h1-3H,(H,10,11)(H,12,13)(H,14,15)
InChIKeyUJMDYLWCYJJYMO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)c1cccc(C(O)=O)c1C(O)=O
ACDLabs 12.01O=C(O)c1cccc(C(=O)O)c1C(=O)O
OpenEye OEToolkits 1.7.6c1cc(c(c(c1)C(=O)O)C(=O)O)C(=O)O
FormulaC9 H6 O6
Namebenzene-1,2,3-tricarboxylic acid
ChEMBLCHEMBL1161013
DrugBank
ZINCZINC000000388710
PDB chain4r3n Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r3n A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway.
Resolution1.35 Å
Binding residue
(original residue number in PDB)		S74 T95 S96 R99 N127 K223
Binding residue
(residue number reindexed from 1)		S73 T94 S95 R98 N126 K222
Annotation score1
Binding affinityMOAD: Ki=1mM
Enzymatic activity
Catalytic site (original residue number in PDB) C128 Q155 R245 H252
Catalytic site (residue number reindexed from 1) C127 Q154 R244 H251
Enzyme Commision number 1.2.1.11: aspartate-semialdehyde dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
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: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:4r3n, PDBe:4r3n, PDBj:4r3n
PDBsum4r3n
PubMed25478842
UniProtQ8DQ00

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