Structure of PDB 6y87 Chain A Binding Site BS01

Receptor Information

>6y87 Chain A (length=470) Species: 287 (Pseudomonas aeruginosa)

PMDFSINPPQRIVFVGLGTIAQSFLPLLSKVHDLSTLEIYAIDPKTPPLI
EYFANSFGLKFINSAIDQINYRDILVPILGEGTVLINLSTDVSSLALIEL
CRSAGALYLDTCIEPWKGGYDDPTIPLHKRTNYHLREQMLSLKKRLGSGV
TALVAHGANPGLVSHFVKRALLDLAEEILGDCKKPSNKEQWAILSQRLGV
KVIHVAEYDSQISQKSRERGEFVNTWSVHGFISESQQPAELGWGSHERSL
PTDASMHTDGCGAAIYIEKPGASVRVKTWTPFNGPSLGYLVTHHEAISIA
DFLTLRTADETYRPTVHYAYRPSDEAILSVHEWFGNDCMTPEKTKVLRPG
DILSGSDYLGVLLMGHEKSSYWYGSILSIEKAKELATLNTATTLQVAAGV
LSGYLWILSHPSAGIIEAEDMDHEVALSYISQYLGELKGVYSDWNPTKNN
PGTFSAIDSDSPWLFSNFVL

Ligand information

• Ligand ID: NAD
• 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:
  CACTVS 3.341: 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)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: 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)ncnc45)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: c1cc(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)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 6y87 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y87 Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): G17 T18 I19 D42 P43 I65 L87 S88 T89 V91 T110 C111 G156 A157 N158 P159 V395
• Binding residue (residue number reindexed from 1): G18 T19 I20 D43 P44 I66 L88 S89 T90 V92 T111 C112 G157 A158 N159 P160 V396
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.5.1.44: homospermidine synthase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016740 transferase activity
• GO:0047296 homospermidine synthase activity

External links

• PDB: RCSB:6y87, PDBe:6y87, PDBj:6y87
• PDBsum: 6y87
• PubMed: 34605434
• UniProt: Q6X2Y9