Structure of PDB 5fi3 Chain A Binding Site BS01

Receptor Information

>5fi3 Chain A (length=344) Species: 4058 (Catharanthus roseus)

VYPVKAFGLAAKDSSGLFSPFNFSRRATGEHDVQLKVLYCGTCQYDREMS
KNKFGFTSYPYVLGHEIVGEVTEVGSKVQKFKVGDKVGVASIIETCGKCE
MCTNEVENYCPEAGSIDSNYGACSNIAVINENFVIRWPENLPLDSGVPLL
CAGITAYSPMKRYGLDKPGKRIGIAGLGGLGHVALRFAKAFGAKVTVISS
SLKKKREAFEKFGADSFLVSSNPEEMQGAAGTLDGIIDTIPGNHSLEPLL
ALLKPLGKLIILGAPEMPFEVPAPSLLMGGKVMAASTAGSMKEIQEMIEF
AAEHNIVADVEVISIDYVNTAMERLDNSDVRYRFVIDIGNTLKS

Ligand information

• Ligand ID: NAP
• InChI: InChI=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
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(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 3.341: NC(=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 3.341: 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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]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)OP(=O)(O)O)O)O)O)C(=O)N
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 5fi3 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5fi3 Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): Q55 E59 T166 G187 L188 G189 G190 L191 S210 S211 K215 T250 I251 P252 L273 G274 T298 S339
• Binding residue (residue number reindexed from 1): Q44 E48 T155 G176 L177 G178 G179 L180 S199 S200 K204 T239 I240 P241 L262 G263 T287 S328
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C54 Q55 Y56 E59 H76 E77 C107 C110 C113 C121 G125 C162 R344
• Catalytic site (residue number reindexed from 1): C43 Q44 Y45 E48 H65 E66 C96 C99 C102 C110 G114 C151 R333

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008270 zinc ion binding
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0045551 cinnamyl-alcohol dehydrogenase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009809 lignin biosynthetic process

External links

• PDB: RCSB:5fi3, PDBe:5fi3, PDBj:5fi3
• PDBsum: 5fi3
• PubMed: 27418042
• UniProt: A0A0F6SD02