Structure of PDB 1pl8 Chain A Binding Site BS02

Receptor Information

>1pl8 Chain A (length=356) Species: 9606 (Homo sapiens)

AAAAKPNNLSLVVHGPGDLRLENYPIPEPGPNEVLLRMHSVGICGSDVHY
WEYGRIGNFIVKKPMVLGHEASGTVEKVGSSVKHLKPGDRVAIEPGAPRE
NDEFCKMGRYNLSPSIFFCATPPDDGNLCRFYKHNAAFCYKLPDNVTFEE
GALIEPLSVGIHACRRGGVTLGHKVLVCGAGPIGMVTLLVAKAMGAAQVV
VTDLSATRLSKAKEIGADLVLQISKESPQEIARKVEGQLGCKPEVTIECT
GAEASIQAGIYATRSGGTLVLVGLGSEMTTVPLLHAAIREVDIKGVFRYC
NTWPVAISMLASKSVNVKPLVTHRFPLEKALEAFETFKKGLGLKIMLKCD
PSDQNP

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: 1pl8 Chain A Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1pl8 X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G181 P182 I183 D203 L204 R208 C249 T250 V272 G273 L274 R298
• Binding residue (residue number reindexed from 1): G181 P182 I183 D203 L204 R208 C249 T250 V272 G273 L274 R298
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C44 G45 S46 H49 H69 E70 R99 D102 C105 S113 F117 P156 G160 K344
• Catalytic site (residue number reindexed from 1): C44 G45 S46 H49 H69 E70 R99 D102 C105 S113 F117 P156 G160 K344
• Enzyme Commision number: 1.1.1.-
  1.1.1.14: L-iditol 2-dehydrogenase.
  1.1.1.4: (R,R)-butanediol dehydrogenase.
  1.1.1.56: ribitol 2-dehydrogenase.
  1.1.1.9: D-xylulose reductase.

Gene Ontology

Molecular Function

• GO:0000721 (R,R)-butanediol dehydrogenase activity
• GO:0003824 catalytic activity
• GO:0003939 L-iditol 2-dehydrogenase (NAD+) activity
• 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:0030246 carbohydrate binding
• GO:0042802 identical protein binding
• GO:0046526 D-xylulose reductase activity
• GO:0046872 metal ion binding
• GO:0047833 D-sorbitol dehydrogenase (acceptor) activity
• GO:0050255 ribitol 2-dehydrogenase (NAD+) activity
• GO:0051287 NAD binding

Biological Process

• GO:0006006 glucose metabolic process
• GO:0006060 sorbitol metabolic process
• GO:0006062 sorbitol catabolic process
• GO:0019640 D-glucuronate catabolic process to D-xylulose 5-phosphate
• GO:0030317 flagellated sperm motility
• GO:0046370 fructose biosynthetic process
• GO:0051160 xylitol catabolic process
• GO:0051164 xylitol metabolic process

Cellular Component

• GO:0005615 extracellular space
• GO:0005739 mitochondrion
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0031514 motile cilium
• GO:0031966 mitochondrial membrane
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:1pl8, PDBe:1pl8, PDBj:1pl8
• PDBsum: 1pl8
• PubMed: 12962626
• UniProt: Q00796|DHSO_HUMAN Sorbitol dehydrogenase (Gene Name=SORD)