Structure of PDB 3cos Chain C Binding Site BS03

Receptor Information

>3cos Chain C (length=379) Species: 9606 (Homo sapiens)

GTKGKVIKCKAAIAWEAGKPLCIEEVEVAPPKAHEVRIQIIATSLCHTDA
TVIDSKFEGLAFPVIVGHEAAGIVESIGPGVTNVKPGDKVIPLYAPLCRK
CKFCLSPLTNLCGKISNLKSPASDQQLMEDKTSRFTCKGKPVYHFFGTST
FSQYTVVSDINLAKIDDDANLERVCLLGCGFSTGYGAAINNAKVTPGSTC
AVFGLGGVGLSAVMGCKAAGASRIIGIDINSEKFVKAKALGATDCLNPRD
LHKPIQEVIIELTKGGVDFALDCAGGSETMKAALDCTTAGWGSCTFIGVA
AGSKGLTVFPEELIIGRTINGTFFGGWKSVDSIPKLVTDYKNKKFNLDAL
VTHTLPFDKISEAFDLMNQGKSIRTILIF

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: 3cos Chain C Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3cos Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): H48 T49 C180 T184 G205 G207 V209 D229 I230 K234 A275 T280 I298 G299 V300 F324 R375
• Binding residue (residue number reindexed from 1): H47 T48 C179 T183 G204 G206 V208 D228 I229 K233 A274 T279 I297 G298 V299 F323 R374
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C47 H48 T49 T52 H69 E70 C99 C102 C105 C113 S117 C180 T184 R375
• Catalytic site (residue number reindexed from 1): C46 H47 T48 T51 H68 E69 C98 C101 C104 C112 S116 C179 T183 R374
• 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:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016491 oxidoreductase activity
• GO:0018479 benzaldehyde dehydrogenase (NAD+) activity
• GO:0019841 retinol binding
• GO:0046872 metal ion binding
• GO:0051287 NAD binding
• GO:0051903 S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity

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:0046164 alcohol catabolic process
• GO:0046294 formaldehyde catabolic process
• GO:1901661 quinone metabolic process

Cellular Component

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

External links

• PDB: RCSB:3cos, PDBe:3cos, PDBj:3cos
• PDBsum: 3cos
• UniProt: P08319|ADH4_HUMAN All-trans-retinol dehydrogenase [NAD(+)] ADH4 (Gene Name=ADH4)