Structure of PDB 5v96 Chain D Binding Site BS02

Receptor Information

>5v96 Chain D (length=465) Species: 5763 (Naegleria fowleri)

TIEYQVKDMSLASLGRKRIEMAEKEMPGLMACRAKYGEEKPLNGVRITGS
LHMTVETAVLIETLKAIGGNIRWCSCNIFSTQDDAAAAIAAANTPVFAWK
GETLVEYWECTWKAIRFGPYQGPQLIVDDGGDATLLIHRGFQAEKEPSIL
DEDGGVEELRIVNNLLKRILKEEPGFFSKIVPDIKGVSEETTTGVHRLYA
MQKQGTLLFPAINVNDSVTKSKFDNIYGCRHSLLDGLNRATDVMLAGKEC
VICGFGDVGKGCAEALKGQGARVIVTEIDPINALQACMAGYTVKTVEDCL
ATADIYVTATGNKDIITLDHMKKMKDMAIICNIGHFDNEIDVLGLKTCEG
VKEINIKPQVDQFLFPDGHSIILLAQGRLVNLGCATGHPAFVMSASFTNQ
TLAQISLWKDKYEIGVYTLPKVLDEEVARLHLEKLGAKLTKLTTSQADYI
GVNANGPYKADHYRY

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: 5v96 Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v96 Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): T198 T199 T200 N232 G261 G263 D264 V265 E284 I285 N289 T317 N319 I322 I340 G341 N388 H395
• Binding residue (residue number reindexed from 1): T191 T192 T193 N225 G254 G256 D257 V258 E277 I278 N282 T310 N312 I315 I333 G334 N381 H388
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): E197 N222 K227 D231 N232 C236 H342 H395 S403 Q407
• Catalytic site (residue number reindexed from 1): E190 N215 K220 D224 N225 C229 H335 H388 S396 Q400
• Enzyme Commision number: 3.13.2.1: adenosylhomocysteinase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004013 adenosylhomocysteinase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0006730 one-carbon metabolic process
• GO:0033353 S-adenosylmethionine cycle

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5v96, PDBe:5v96, PDBj:5v96
• PDBsum: 5v96
• UniProt: A0A1Z0YU84