Structure of PDB 1e3l Chain B Binding Site BS01

Receptor Information

>1e3l Chain B (length=373) Species: 10090 (Mus musculus)

GKVIKCKAAIAWKTGSPLCIEEIEVSPPKACEVRIQVIATCVCHTDINAT
DPKKKALFPVVLGHECAGIVESVGPGVTNFKPGDKVIPFFAPQCKRCKLC
LSPLTNLCGKLRNFKYPTIDQELMEDRTSRFTCKGRSIYHFMGVSSFSQY
TVVSEANLARVDDEANLERVCLIGCGFSSGYGAAINTAKVTPGSTCAVFG
LGCVGLSAIIGCKIAGASRIIAIDINGEKFPKAKALGATDCLNPRELDKP
VQDVITELTAGGVDYSLDCAGTAQTLKAAVDCTVLGWGSCTVVGAKVDEM
TIPTVDVILGRSINGTFFGGWKSVDSVPNLVSDYKNKKFDLDLLVTHALP
FESINDAIDLMKEGKSIRTILTF

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: 1e3l Chain B Residue 378

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1e3l Crystal Structure of Mouse Class II Alcohol Dehydrogenase Reveal Determinants of Substrate Specificity and Catalytic Efficiency
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): H47 S182 G203 G205 V207 D227 I228 T278 V296 G297 F320 F321
• Binding residue (residue number reindexed from 1): H44 S179 G200 G202 V204 D224 I225 T275 V293 G294 F317 F318
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C46 H47 T48 N51 H67 E68 C97 C100 C103 C111 R115 C178 S182 R371
• Catalytic site (residue number reindexed from 1): C43 H44 T45 N48 H64 E65 C94 C97 C100 C108 R112 C175 S179 R368
• Enzyme Commision number: 1.1.1.105: all-trans-retinol dehydrogenase (NAD(+)).

Gene Ontology

Molecular Function

• GO:0003960 NADPH:quinone reductase activity
• GO:0004022 alcohol dehydrogenase (NAD+) activity
• GO:0004032 aldose reductase (NADPH) activity
• GO:0004745 all-trans-retinol dehydrogenase (NAD+) activity
• GO:0005503 all-trans retinal 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:0018479 benzaldehyde dehydrogenase (NAD+) activity
• GO:0019841 retinol binding
• GO:0046872 metal ion binding
• GO:0051287 NAD binding

Biological Process

• GO:0001523 retinoid metabolic process
• GO:0006066 alcohol metabolic process
• GO:0006067 ethanol metabolic process
• GO:0006081 cellular aldehyde metabolic process
• GO:0006629 lipid metabolic process
• GO:0010430 fatty acid omega-oxidation
• GO:0042572 retinol metabolic process
• GO:0044282 small molecule catabolic process
• GO:0046164 alcohol catabolic process
• GO:1901661 quinone metabolic process

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1e3l, PDBe:1e3l, PDBj:1e3l
• PDBsum: 1e3l
• PubMed: 10970744
• UniProt: Q9QYY9|ADH4_MOUSE All-trans-retinol dehydrogenase [NAD(+)] ADH4 (Gene Name=Adh4)