Structure of PDB 4mpd Chain A Binding Site BS01

Receptor Information

>4mpd Chain A (length=318) Species: 196620 (Staphylococcus aureus subsp. aureus MW2)

REMLYLNRSDIEQAGGNHSQVYVDALTEALTAHAHNDFVQPLKPYLRQAD
RIIAMPSHIISGIKWIGSKHDNPSKRNMERASGVIILNDPETNYPIAVME
ASLISSMRTAAVSVIAAKHLAKKGFKDLTIIGCGLIGDKQLQSMLEQFDH
IERVFVYDQFSEACARFVDRWQQQRPEINFIATENAKEAVSNGEVVITCT
VTDQPYIEYDWLQKGAFISNISIMDVHKEVFIKADKVVVDDWSQCNTINQ
LVLEGKFSKEALHAELGQLVTGDIPGREDDDEIILLNPMGMAIEDISSAY
FIYQQAQQQNIGTTLNLY

Ligand information

• Ligand ID: NAJ
• InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.7.5: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)([O-])OCC3C(C(C(O3)n4cnc5c4nc[nH+]c5N)O)O)O)O)C(=O)N
  OpenEye OEToolkits 1.7.5: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])OP(=O)([O-])OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4nc[nH+]c5N)O)O)O)O)C(=O)N
  CACTVS 3.385: NC(=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)[C@@H]3O)n4cnc5c(N)[nH+]cnc45)[C@@H](O)[C@H]2O
  CACTVS 3.385: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P]([O-])(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)[nH+]cnc45)[CH](O)[CH]2O
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 4mpd Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4mpd Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor.
• Resolution: 2.101 Å
• Binding residue (original residue number in PDB): R94 R122 T123 G148 I150 D172 Q173 F174 T214 V215 I235
• Binding residue (residue number reindexed from 1): R80 R108 T109 G134 I136 D158 Q159 F160 T200 V201 I221
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): I62 M238
• Catalytic site (residue number reindexed from 1): I53 M224

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor

Biological Process

• GO:0019290 siderophore biosynthetic process

External links

• PDB: RCSB:4mpd, PDBe:4mpd, PDBj:4mpd
• PDBsum: 4mpd
• PubMed: 24485762
• UniProt: A0A0H3K9Y6