Structure of PDB 1yqx Chain B Binding Site BS03

Receptor Information

>1yqx Chain B (length=359) Species: 3693 (Populus tremuloides)

SPEEEHPVKAFGWAARDQSGHLSPFNFSRRATGEEDVRFKVLYCGVCHSD
LHSIKNDWGFSMYPLVPGHEIVGEVTEVGSKVKKVNVGDKVGVGCLVGAC
HSCESCANDLENYCPKMILTYASIYHDGTITYGGYSNHMVANERYIIRFP
DNMPLDGGAPLLCAGITVYSPLKYFGLDEPGKHIGIVGLGGLGHVAVKFA
KAFGSKVTVISTSPSKKEEALKNFGADSFLVSRDQEQMQAAAGTLDGIID
TVSAVHPLLPLFGLLKSHGKLILVGAPEKPLELPAFSLIAGRKIVAGSGI
GGMKETQEMIDFAAKHNITADIEVISTDYLNTAMERLAKNDVRYRFVIDV
GNTLAATKP

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: 1yqx Chain B Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yqx Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): C50 H51 S52 H55 C166 T170 G191 L192 G193 G194 L195 S214 T215 S216 K219 T254 V255 S256 V277 G278 A279 G302 I303 N343
• Binding residue (residue number reindexed from 1): C47 H48 S49 H52 C163 T167 G188 L189 G190 G191 L192 S211 T212 S213 K216 T251 V252 S253 V274 G275 A276 G299 I300 N340
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C50 H51 S52 H55 H72 E73 C103 C106 C109 C117 I121 C166 T170 R348
• Catalytic site (residue number reindexed from 1): C47 H48 S49 H52 H69 E70 C100 C103 C106 C114 I118 C163 T167 R345
• Enzyme Commision number: 1.1.1.195: cinnamyl-alcohol dehydrogenase.

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:1yqx, PDBe:1yqx, PDBj:1yqx
• PDBsum: 1yqx
• PubMed: 15829607
• UniProt: Q94G59