Structure of PDB 4r3n Chain A Binding Site BS01

Receptor Information
>4r3n Chain A (length=357) 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
TFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTA
ELKFELK
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain4r3n Chain A Residue 403 [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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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)		G9 T11 G12 A13 V14 A36 S37 S40 T57 S71 A72 G73 N94 T95 N127 C128 G161 M162 G329
Binding residue
(residue number reindexed from 1)		G8 T10 G11 A12 V13 A35 S36 S39 T56 S70 A71 G72 N93 T94 N126 C127 G160 M161 G328
Annotation score4
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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